{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "### Running in Docker container on Ostrich\n", "\n", "#### Started Docker container with the following command:\n", "\n", "```docker run -p 8888:8888 -v /Users/sam/data/:/data -v /Users/sam/owl_home/:/owl_home -v /Users/sam/owl_web/:/owl_web -v /Users/sam/gitrepos:/gitrepos -it f99537d7e06a```\n", "\n", "The command allows access to Jupyter Notebook over port 8888 and makes my Jupyter Notebook GitHub repo and my data files on Owl/home and Owl/web accessible to the Docker container.\n", "\n", "Once the container was started, started Jupyter Notebook with the following command inside the Docker container:\n", "\n", "```jupyter notebook```\n", "\n", "This is configured in the Docker container to launch a Jupyter Notebook without a browser on port 8888.\n", "\n", "The Docker container is running on an image created from this [Dockerfile (Git commit 443bc42)](https://github.com/sr320/LabDocs/blob/443bc425cd36d23a07cf12625f38b7e3a397b9be/code/dockerfiles/Dockerfile.bio)" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Mon Mar 6 16:47:23 UTC 2017\n" ] } ], "source": [ "%%bash\n", "date" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Check computer specs" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "0f2bca9c664b\n" ] } ], "source": [ "%%bash\n", "hostname" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Architecture: x86_64\n", "CPU op-mode(s): 32-bit, 64-bit\n", "Byte Order: Little Endian\n", "CPU(s): 8\n", "On-line CPU(s) list: 0-7\n", "Thread(s) per core: 1\n", "Core(s) per socket: 8\n", "Socket(s): 1\n", "Vendor ID: GenuineIntel\n", "CPU family: 6\n", "Model: 26\n", "Model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz\n", "Stepping: 5\n", "CPU MHz: 2260.998\n", "BogoMIPS: 4521.99\n", "Hypervisor vendor: KVM\n", "Virtualization type: full\n", "L1d cache: 32K\n", "L1i cache: 32K\n", "L2 cache: 256K\n", "L3 cache: 8192K\n" ] } ], "source": [ "%%bash\n", "lscpu" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Copy demultiplexed BGI FASTQ files to local computer (Ostrich) and verfiy checksums" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "\u001b[0m\u001b[34;42m160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc\u001b[0m/\r\n", "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "\u001b[34;42m160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc\u001b[0m/\r\n", 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"\u001b[01;32mUnKnow_1.fq.gz\u001b[0m*\r\n", "\u001b[01;32mUnKnow_2.fq.gz\u001b[0m*\r\n", "\u001b[01;32mbgi_project_summary.tar.gz\u001b[0m*\r\n", "checksums.md5\r\n", "index.lst\r\n", "\u001b[01;32mmd5.check\u001b[0m*\r\n", "\u001b[01;32mmd5.txt\u001b[0m*\r\n", "md51.txt\r\n", "readme.md\r\n", "split.sh\r\n" ] } ], "source": [ "ls /owl_web/nightingales/O_lurida/20160223_gbs/" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mkdir /data/20170306_fastqc_gbs" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/data/20170306_fastqc_gbs\n" ] } ], "source": [ "cd /data/20170306_fastqc_gbs/" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t25m31.705s\n", "user\t0m0.070s\n", "sys\t4m9.310s\n" ] } ], "source": [ "%%bash\n", "time for file in /owl_web/nightingales/O_lurida/20160223_gbs/1[HNS]*.gz\n", " do\n", " cp \"$file\" .\n", " done" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The code above uses looks for all gzipped files (.gz) that start with \"1\", followed by either a \"H\", \"N\", or \"S\"." ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "247\r\n" ] } ], "source": [ "ls -1 | wc -l" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "ARRRGGHH! My connection crashed during the copy command and I forgot that I needed to change to the working directory specified in Input 7 above... That explains why the ```ls -1 | wc -l``` has so many files. Going to move them over to my desired directory." ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t12m25.731s\n", "user\t0m1.040s\n", "sys\t4m9.830s\n" ] } ], "source": [ "%%bash\n", "time for file in /owl_web/nightingales/O_lurida/20160223_gbs/1[HNS]*.gz\n", " do\n", " mv \"$file\" /data/20170306_fastqc_gbs/\n", " done" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/data/20170306_fastqc_gbs\n" ] } ], "source": [ "cd /data/20170306_fastqc_gbs/" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "193\r\n" ] } ], "source": [ "ls -1 | wc -l" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Hmmm, I was expecting 192 files (96 samples x 2 files per sample). Let's see what's going on." ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 29095420\r\n", "-rwxrwxrwx 1 srlab staff 154481135 Feb 19 2016 \u001b[0m\u001b[01;32m1HL_10A_1.fq.gz\u001b[0m*\r\n", "-rwxrwxrwx 1 srlab staff 193383163 Feb 19 2016 \u001b[01;32m1HL_10A_2.fq.gz\u001b[0m*\r\n", "-rwxrwxrwx 1 srlab staff 172568431 Feb 19 2016 \u001b[01;32m1HL_11A_1.fq.gz\u001b[0m*\r\n", "-rwxrwxrwx 1 srlab staff 215945074 Feb 19 2016 \u001b[01;32m1HL_11A_2.fq.gz\u001b[0m*\r\n", "-rwxrwxrwx 1 srlab staff 121896571 Feb 19 2016 \u001b[01;32m1HL_12A_1.fq.gz\u001b[0m*\r\n", "-rwxrwxrwx 1 srlab staff 153769201 Feb 19 2016 \u001b[01;32m1HL_12A_2.fq.gz\u001b[0m*\r\n", "-rwxrwxrwx 1 srlab staff 129166835 Feb 19 2016 \u001b[01;32m1HL_13A_1.fq.gz\u001b[0m*\r\n", "-rwxrwxrwx 1 srlab staff 162561925 Feb 19 2016 \u001b[01;32m1HL_13A_2.fq.gz\u001b[0m*\r\n", "-rwxrwxrwx 1 srlab staff 96637858 Feb 19 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\u001b[01;32m1SN_8A_2.fq.gz\u001b[0m*\r\n", "-rwxrwxrwx 1 srlab staff 155816621 Feb 19 2016 \u001b[01;32m1SN_9A_1.fq.gz\u001b[0m*\r\n", "-rwxrwxrwx 1 srlab staff 192919423 Feb 19 2016 \u001b[01;32m1SN_9A_2.fq.gz\u001b[0m*\r\n", "-rw-r--r-- 1 srlab staff 9548 Mar 6 17:26 temp_checksums.md5\r\n" ] } ], "source": [ "ls -l" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Ahhhh! That temp_checksums.md5 file must've been created before my computer crashed (I had started a series of cells to just process all the steps I wanted and the MD5 creation was one of them). Let's see if that command actually completed." ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "ename": "SyntaxError", "evalue": "invalid syntax (, line 1)", "output_type": "error", "traceback": [ "\u001b[0;36m File \u001b[0;32m\"\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m wc -l temp_checksums.md5\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n" ] } ], "source": [ "wc -l temp_checksums.md5" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "192 temp_checksums.md5\n" ] } ], "source": [ "%%bash\n", "wc -l temp_checksums.md5" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "57875c749f21bed3d4e6619ef53596b7 1HL_10A_1.fq.gz\n", "3d87907131c5bcca146a2e1eb82ceb92 1HL_10A_2.fq.gz\n", "bd666574d447d79b2607bfa182aeb754 1HL_11A_1.fq.gz\n", "8053d67c5575b040708510ddc02c5123 1HL_11A_2.fq.gz\n", "719547253c42a1c3690015014bda0f89 1HL_12A_1.fq.gz\n", "6f837d3464573b30df9e7f67867491ae 1HL_12A_2.fq.gz\n", "8772f45a2bcf1f7aa6669e027f25bcd5 1HL_13A_1.fq.gz\n", "8914728623f52930aa88b15cece20d08 1HL_13A_2.fq.gz\n", "91acc4b1d196b739be2bde44b14436c9 1HL_14A_1.fq.gz\n", "0c7b91215e2ee08dabde2fa5ce311b34 1HL_14A_2.fq.gz\n", "be7c9d91bf5895b489a09989fe0c3d55 1SN_5A_1.fq.gz\n", "02bd1ff849c4edf635c866e41f4ac158 1SN_5A_2.fq.gz\n", "eeeb78e7d9f73ab67bb4c5325ceb29d0 1SN_6A_1.fq.gz\n", "28a761d01540930600fd4cb412367e65 1SN_6A_2.fq.gz\n", "ea6036ddc236793fddc9ee4c12615b70 1SN_7A_1.fq.gz\n", "21a1b9bebedecf9043d1529d48ba461f 1SN_7A_2.fq.gz\n", "d29170e28d64b4dea984b31ff933c482 1SN_8A_1.fq.gz\n", "94a786839caa3498da6e7cbd4b27496c 1SN_8A_2.fq.gz\n", "659e9e5cce523f14de81da86daf4c38c 1SN_9A_1.fq.gz\n", "5d77c5fd542657141e39e83d632948b6 1SN_9A_2.fq.gz\n" ] } ], "source": [ "%%bash\n", "head temp_checksums.md5\n", "tail temp_checksums.md5" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Generate MD5 checksums & compare to original checksums" ] }, { "cell_type": "markdown", "metadata": { "collapsed": true }, "source": [ "This command already ran, so I'm just posting the code I used to generate the checksums for posterity:\n", "\n", "```\n", "%%bash\n", "time for file in *.gz\n", " do\n", " md5sum \"$file\" >> temp_checksums.md5\n", " done\n", "```" ] }, { "cell_type": "markdown", "metadata": { "collapsed": true }, "source": [ "The checksums look complete, so I'll go ahead and compare them with the original checksums on Owl." ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "MD5 (1HL_10A_1.fq.gz) = 57875c749f21bed3d4e6619ef53596b7\n", "MD5 (1HL_10A_2.fq.gz) = 3d87907131c5bcca146a2e1eb82ceb92\n", "MD5 (1HL_11A_1.fq.gz) = bd666574d447d79b2607bfa182aeb754\n", "MD5 (1HL_11A_2.fq.gz) = 8053d67c5575b040708510ddc02c5123\n", "MD5 (1HL_12A_1.fq.gz) = 719547253c42a1c3690015014bda0f89\n", "MD5 (1HL_12A_2.fq.gz) = 6f837d3464573b30df9e7f67867491ae\n", "MD5 (1HL_13A_1.fq.gz) = 8772f45a2bcf1f7aa6669e027f25bcd5\n", "MD5 (1HL_13A_2.fq.gz) = 8914728623f52930aa88b15cece20d08\n", "MD5 (1HL_14A_1.fq.gz) = 91acc4b1d196b739be2bde44b14436c9\n", "MD5 (1HL_14A_2.fq.gz) = 0c7b91215e2ee08dabde2fa5ce311b34\n" ] } ], "source": [ "%%bash\n", "head /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let's write these values to a temp file in our current directory (/data/20170306_fastqc_gbs) for ease of comparison. Will have to tweak the formatting to match, too..." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "First, let's try to pull out a desired record from the target file using ```grep``` and the ```-e``` (for regular expression pattern matching)." ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": false }, "outputs": [ { "ename": "SyntaxError", "evalue": "invalid syntax (, line 1)", "output_type": "error", "traceback": [ "\u001b[0;36m File \u001b[0;32m\"\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m grep -e 1HL_10A_1.fq.gz /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n" ] } ], "source": [ "grep -e 1HL_10A_1.fq.gz /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "MD5 (1HL_10A_1.fq.gz) = 57875c749f21bed3d4e6619ef53596b7\n" ] } ], "source": [ "%%bash\n", "grep -e 1HL_10A_1.fq.gz /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Test out some formatting options...\n", "\n", "The command below will use the ```grep``` from above to pull the desired record.\n", "\n", "It pipes the result from ```grep``` to the translate (```tr```) command.\n", "\n", "The ```tr``` command uses the ```-d``` (delete) argument to delete anything indicated in the single quotes that follow.\n", "\n", "The result from that is then piped to ```awk```.\n", "\n", "```awk``` prints the fourth field (```$4``` i.e. column), followed by the contents of the second field (```$2```)." ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "57875c749f21bed3d4e6619ef53596b71HL_10A_1.fq.gz\n" ] } ], "source": [ "%%bash\n", "grep -e 1HL_10A_1.fq.gz /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 | \\\n", "tr -d '()' | \\\n", "awk '{ print $4 $2}'" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "OK, I didn't specify a field separator for the output, so the content of the two columns is adjacent instead of separated by some whitespace. The whitespace is actually two consecutive spaces, so I've added this to the ```awk``` print statement: \" \"" ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "57875c749f21bed3d4e6619ef53596b7 1HL_10A_1.fq.gz\n" ] } ], "source": [ "%%bash\n", "grep -e 1HL_10A_1.fq.gz /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 | \\\n", "tr -d '()' | \\\n", "awk '{ print $4 \" \" $2}'" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "OK, that looks good. Will write to temp file for use in MD5 checksum comparison." ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Process is interrupted.\n" ] } ], "source": [ "%%bash\n", "grep -e 1[HNS]*.fq.gz /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 | \\\n", "tr -d '()' | \\\n", "awk '{ print $4 \" \" $2}' > owl_checksums.md5" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "I killed the above command because I didn't format the grep command properly." ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "grep \"1[HNS]*.fq.gz\" /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 | \\\n", "tr -d '()' | \\\n", "awk '{ print $4 \" \" $2}' > owl_checksums.md5" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "98 owl_checksums.md5\n", "57875c749f21bed3d4e6619ef53596b7 1HL_10A_1.fq.gz\n", "bd666574d447d79b2607bfa182aeb754 1HL_11A_1.fq.gz\n", "719547253c42a1c3690015014bda0f89 1HL_12A_1.fq.gz\n", "8772f45a2bcf1f7aa6669e027f25bcd5 1HL_13A_1.fq.gz\n", "91acc4b1d196b739be2bde44b14436c9 1HL_14A_1.fq.gz\n", "e532bf27cd835ddc888b25fab8e12d58 1HL_15A_1.fq.gz\n", "bc7c5ba1c87cb972c087b545db29d378 1HL_16A_1.fq.gz\n", "1e06f736f4d19fe6d09e903243284eda 1HL_17A_1.fq.gz\n", "5051f00e153277d732e83e2742b1e2f6 1HL_19A_1.fq.gz\n", "5bf8732899249f7ce103bf4f5c182180 1HL_1A_1.fq.gz\n", "89fee054c43e95cc4f368f4bde3359bf 1SN_32A_1.fq.gz\n", "ba0ad341e401cf3c08db713fc2ccf95b 1SN_3A_1.fq.gz\n", "52405bdd6e3aaa34966bb3edf202f994 1SN_4A_1.fq.gz\n", "be7c9d91bf5895b489a09989fe0c3d55 1SN_5A_1.fq.gz\n", "eeeb78e7d9f73ab67bb4c5325ceb29d0 1SN_6A_1.fq.gz\n", "ea6036ddc236793fddc9ee4c12615b70 1SN_7A_1.fq.gz\n", "d29170e28d64b4dea984b31ff933c482 1SN_8A_1.fq.gz\n", "659e9e5cce523f14de81da86daf4c38c 1SN_9A_1.fq.gz\n", "5b3d8d5ea6b82b6c27d87c8813e87c6d UnKnow_1.fq.gz\n", "afd18614b9f5694af1a59672821cd0db /Volumes/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n" ] } ], "source": [ "%%bash\n", "wc -l owl_checksums.md5\n", "head owl_checksums.md5\n", "tail owl_checksums.md5" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Ah! Two, too many! I realize this is because the some of the checksum values match the grep pattern!! Let's re-run it with some changes to the grep pattern..." ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "grep \"1[HNS][FLN]*.fq.gz\" /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 | \\\n", "tr -d '()' | \\\n", "awk '{ print $4 \" \" $2}' > owl_checksums.md5" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "0 owl_checksums.md5\n" ] } ], "source": [ "%%bash\n", "wc -l owl_checksums.md5\n", "head owl_checksums.md5\n", "tail owl_checksums.md5" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Hmmm, that's odd. Do I have to escape the periods in the filenames?" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "grep \"1[HNS][FLN]_*\\.fq\\.gz\" /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 | \\\n", "tr -d '()' | \\\n", "awk '{ print $4 \" \" $2}' > owl_checksums.md5" ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "0 owl_checksums.md5\n" ] } ], "source": [ "%%bash\n", "wc -l owl_checksums.md5\n", "head owl_checksums.md5\n", "tail owl_checksums.md5" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "I think the asterisk is causing issues (possibly because it's interpreted as regex asterisk (match preceding character), instead of as shell globbing (expand asterisk to match all characters)." ] }, { "cell_type": "code", "execution_count": 24, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "grep \"1[HNS][FLN]\" /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5 | \\\n", "tr -d '()' | \\\n", "awk '{ print $4 \" \" $2}' > owl_checksums.md5" ] }, { "cell_type": "code", "execution_count": 25, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "192 owl_checksums.md5\n", "57875c749f21bed3d4e6619ef53596b7 1HL_10A_1.fq.gz\n", "3d87907131c5bcca146a2e1eb82ceb92 1HL_10A_2.fq.gz\n", "bd666574d447d79b2607bfa182aeb754 1HL_11A_1.fq.gz\n", "8053d67c5575b040708510ddc02c5123 1HL_11A_2.fq.gz\n", "719547253c42a1c3690015014bda0f89 1HL_12A_1.fq.gz\n", "6f837d3464573b30df9e7f67867491ae 1HL_12A_2.fq.gz\n", "8772f45a2bcf1f7aa6669e027f25bcd5 1HL_13A_1.fq.gz\n", "8914728623f52930aa88b15cece20d08 1HL_13A_2.fq.gz\n", "91acc4b1d196b739be2bde44b14436c9 1HL_14A_1.fq.gz\n", "0c7b91215e2ee08dabde2fa5ce311b34 1HL_14A_2.fq.gz\n", "be7c9d91bf5895b489a09989fe0c3d55 1SN_5A_1.fq.gz\n", "02bd1ff849c4edf635c866e41f4ac158 1SN_5A_2.fq.gz\n", "eeeb78e7d9f73ab67bb4c5325ceb29d0 1SN_6A_1.fq.gz\n", "28a761d01540930600fd4cb412367e65 1SN_6A_2.fq.gz\n", "ea6036ddc236793fddc9ee4c12615b70 1SN_7A_1.fq.gz\n", "21a1b9bebedecf9043d1529d48ba461f 1SN_7A_2.fq.gz\n", "d29170e28d64b4dea984b31ff933c482 1SN_8A_1.fq.gz\n", "94a786839caa3498da6e7cbd4b27496c 1SN_8A_2.fq.gz\n", "659e9e5cce523f14de81da86daf4c38c 1SN_9A_1.fq.gz\n", "5d77c5fd542657141e39e83d632948b6 1SN_9A_2.fq.gz\n" ] } ], "source": [ "%%bash\n", "wc -l owl_checksums.md5\n", "head owl_checksums.md5\n", "tail owl_checksums.md5" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Success! Let's compare the two checksum files." ] }, { "cell_type": "code", "execution_count": 26, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "0\n" ] } ], "source": [ "%%bash\n", "diff owl_checksums.md5 temp_checksums.md5\n", "echo $?" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Beauty! No differences! Now that we're confident the files copied over without issue, we can run FastQC." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### FastQC Analysis" ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/usr/local/bioinformatics/FastQC/fastqc\n" ] } ], "source": [ "%%bash\n", "which fastqc" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "In order to take advantage of the ```--threads``` option (allows you to specify how much memory to assign to each input file; 250MB is allocated to each file), I need to have an option to list all of the FASTQ files. Going to try to store the list of FASTQ files in a shell variable. Have to remove the newlines (the ```\\n``` in the code below) so the list of files is printed horizontally (i.e. separated by a space instead of a newline)." ] }, { "cell_type": "code", "execution_count": 28, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "FASTQ_LIST=\"$(ls -1 *.gz| tr '\\n' ' ')\"" ] }, { "cell_type": "code", "execution_count": 29, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "head $FASTQ_LIST" ] }, { "cell_type": "code", "execution_count": 30, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n" ] } ], "source": [ "%%bash\n", "echo \"$FASTQ_LIST\" | head" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The three cells above show me that the bash variable is not available outside of its individual cell. Let's check it when all the commands are in a single cell." ] }, { "cell_type": "code", "execution_count": 31, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1HL_10A_1.fq.gz 1HL_10A_2.fq.gz 1HL_11A_1.fq.gz 1HL_11A_2.fq.gz 1HL_12A_1.fq.gz 1HL_12A_2.fq.gz 1HL_13A_1.fq.gz 1HL_13A_2.fq.gz 1HL_14A_1.fq.gz 1HL_14A_2.fq.gz 1HL_15A_1.fq.gz 1HL_15A_2.fq.gz 1HL_16A_1.fq.gz 1HL_16A_2.fq.gz 1HL_17A_1.fq.gz 1HL_17A_2.fq.gz 1HL_19A_1.fq.gz 1HL_19A_2.fq.gz 1HL_1A_1.fq.gz 1HL_1A_2.fq.gz 1HL_20A_1.fq.gz 1HL_20A_2.fq.gz 1HL_21A_1.fq.gz 1HL_21A_2.fq.gz 1HL_22A_1.fq.gz 1HL_22A_2.fq.gz 1HL_23A_1.fq.gz 1HL_23A_2.fq.gz 1HL_24A_1.fq.gz 1HL_24A_2.fq.gz 1HL_25A_1.fq.gz 1HL_25A_2.fq.gz 1HL_26A_1.fq.gz 1HL_26A_2.fq.gz 1HL_27A_1.fq.gz 1HL_27A_2.fq.gz 1HL_28A_1.fq.gz 1HL_28A_2.fq.gz 1HL_29A_1.fq.gz 1HL_29A_2.fq.gz 1HL_2A_1.fq.gz 1HL_2A_2.fq.gz 1HL_31A_1.fq.gz 1HL_31A_2.fq.gz 1HL_33A_1.fq.gz 1HL_33A_2.fq.gz 1HL_34A_1.fq.gz 1HL_34A_2.fq.gz 1HL_35A_1.fq.gz 1HL_35A_2.fq.gz 1HL_3A_1.fq.gz 1HL_3A_2.fq.gz 1HL_4A_1.fq.gz 1HL_4A_2.fq.gz 1HL_5A_1.fq.gz 1HL_5A_2.fq.gz 1HL_6A_1.fq.gz 1HL_6A_2.fq.gz 1HL_7A_1.fq.gz 1HL_7A_2.fq.gz 1HL_8A_1.fq.gz 1HL_8A_2.fq.gz 1HL_9A_1.fq.gz 1HL_9A_2.fq.gz 1NF_10A_1.fq.gz 1NF_10A_2.fq.gz 1NF_11A_1.fq.gz 1NF_11A_2.fq.gz 1NF_12A_1.fq.gz 1NF_12A_2.fq.gz 1NF_13A_1.fq.gz 1NF_13A_2.fq.gz 1NF_14A_1.fq.gz 1NF_14A_2.fq.gz 1NF_15A_1.fq.gz 1NF_15A_2.fq.gz 1NF_16A_1.fq.gz 1NF_16A_2.fq.gz 1NF_17A_1.fq.gz 1NF_17A_2.fq.gz 1NF_18A_1.fq.gz 1NF_18A_2.fq.gz 1NF_19A_1.fq.gz 1NF_19A_2.fq.gz 1NF_1A_1.fq.gz 1NF_1A_2.fq.gz 1NF_20A_1.fq.gz 1NF_20A_2.fq.gz 1NF_21A_1.fq.gz 1NF_21A_2.fq.gz 1NF_22A_1.fq.gz 1NF_22A_2.fq.gz 1NF_23A_1.fq.gz 1NF_23A_2.fq.gz 1NF_24A_1.fq.gz 1NF_24A_2.fq.gz 1NF_25A_1.fq.gz 1NF_25A_2.fq.gz 1NF_26A_1.fq.gz 1NF_26A_2.fq.gz 1NF_27A_1.fq.gz 1NF_27A_2.fq.gz 1NF_28A_1.fq.gz 1NF_28A_2.fq.gz 1NF_29A_1.fq.gz 1NF_29A_2.fq.gz 1NF_2A_1.fq.gz 1NF_2A_2.fq.gz 1NF_30A_1.fq.gz 1NF_30A_2.fq.gz 1NF_31A_1.fq.gz 1NF_31A_2.fq.gz 1NF_32A_1.fq.gz 1NF_32A_2.fq.gz 1NF_33A_1.fq.gz 1NF_33A_2.fq.gz 1NF_4A_1.fq.gz 1NF_4A_2.fq.gz 1NF_5A_1.fq.gz 1NF_5A_2.fq.gz 1NF_6A_1.fq.gz 1NF_6A_2.fq.gz 1NF_7A_1.fq.gz 1NF_7A_2.fq.gz 1NF_8A_1.fq.gz 1NF_8A_2.fq.gz 1NF_9A_1.fq.gz 1NF_9A_2.fq.gz 1SN_10A_1.fq.gz 1SN_10A_2.fq.gz 1SN_11A_1.fq.gz 1SN_11A_2.fq.gz 1SN_12A_1.fq.gz 1SN_12A_2.fq.gz 1SN_13A_1.fq.gz 1SN_13A_2.fq.gz 1SN_14A_1.fq.gz 1SN_14A_2.fq.gz 1SN_15A_1.fq.gz 1SN_15A_2.fq.gz 1SN_16A_1.fq.gz 1SN_16A_2.fq.gz 1SN_17A_1.fq.gz 1SN_17A_2.fq.gz 1SN_18A_1.fq.gz 1SN_18A_2.fq.gz 1SN_19A_1.fq.gz 1SN_19A_2.fq.gz 1SN_1A_1.fq.gz 1SN_1A_2.fq.gz 1SN_20A_1.fq.gz 1SN_20A_2.fq.gz 1SN_21A_1.fq.gz 1SN_21A_2.fq.gz 1SN_22A_1.fq.gz 1SN_22A_2.fq.gz 1SN_23A_1.fq.gz 1SN_23A_2.fq.gz 1SN_24A_1.fq.gz 1SN_24A_2.fq.gz 1SN_25A_1.fq.gz 1SN_25A_2.fq.gz 1SN_26A_1.fq.gz 1SN_26A_2.fq.gz 1SN_27A_1.fq.gz 1SN_27A_2.fq.gz 1SN_28A_1.fq.gz 1SN_28A_2.fq.gz 1SN_29A_1.fq.gz 1SN_29A_2.fq.gz 1SN_2A_1.fq.gz 1SN_2A_2.fq.gz 1SN_30A_1.fq.gz 1SN_30A_2.fq.gz 1SN_31A_1.fq.gz 1SN_31A_2.fq.gz 1SN_32A_1.fq.gz 1SN_32A_2.fq.gz 1SN_3A_1.fq.gz 1SN_3A_2.fq.gz 1SN_4A_1.fq.gz 1SN_4A_2.fq.gz 1SN_5A_1.fq.gz 1SN_5A_2.fq.gz 1SN_6A_1.fq.gz 1SN_6A_2.fq.gz 1SN_7A_1.fq.gz 1SN_7A_2.fq.gz 1SN_8A_1.fq.gz 1SN_8A_2.fq.gz 1SN_9A_1.fq.gz 1SN_9A_2.fq.gz \n" ] } ], "source": [ "%%bash\n", "FASTQ_LIST=\"$(ls -1 *.gz| tr '\\n' ' ')\"\n", "echo \"$FASTQ_LIST\" | head" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Yep, that works. Let's run the FastQC command.\n", "\n", "I'm using the following options:\n", "\n", "```--extract```: Doesn't compress the ouput folder.\n", "\n", "```--threads 96```: Use 96 threads to process files (250MB of memory is allocated to each file)\n", "\n", "```--quiet```: Suppresses the stdout and only prints stderr." ] }, { "cell_type": "code", "execution_count": 32, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Skipping '1HL_10A_1.fq.gz 1HL_10A_2.fq.gz 1HL_11A_1.fq.gz 1HL_11A_2.fq.gz 1HL_12A_1.fq.gz 1HL_12A_2.fq.gz 1HL_13A_1.fq.gz 1HL_13A_2.fq.gz 1HL_14A_1.fq.gz 1HL_14A_2.fq.gz 1HL_15A_1.fq.gz 1HL_15A_2.fq.gz 1HL_16A_1.fq.gz 1HL_16A_2.fq.gz 1HL_17A_1.fq.gz 1HL_17A_2.fq.gz 1HL_19A_1.fq.gz 1HL_19A_2.fq.gz 1HL_1A_1.fq.gz 1HL_1A_2.fq.gz 1HL_20A_1.fq.gz 1HL_20A_2.fq.gz 1HL_21A_1.fq.gz 1HL_21A_2.fq.gz 1HL_22A_1.fq.gz 1HL_22A_2.fq.gz 1HL_23A_1.fq.gz 1HL_23A_2.fq.gz 1HL_24A_1.fq.gz 1HL_24A_2.fq.gz 1HL_25A_1.fq.gz 1HL_25A_2.fq.gz 1HL_26A_1.fq.gz 1HL_26A_2.fq.gz 1HL_27A_1.fq.gz 1HL_27A_2.fq.gz 1HL_28A_1.fq.gz 1HL_28A_2.fq.gz 1HL_29A_1.fq.gz 1HL_29A_2.fq.gz 1HL_2A_1.fq.gz 1HL_2A_2.fq.gz 1HL_31A_1.fq.gz 1HL_31A_2.fq.gz 1HL_33A_1.fq.gz 1HL_33A_2.fq.gz 1HL_34A_1.fq.gz 1HL_34A_2.fq.gz 1HL_35A_1.fq.gz 1HL_35A_2.fq.gz 1HL_3A_1.fq.gz 1HL_3A_2.fq.gz 1HL_4A_1.fq.gz 1HL_4A_2.fq.gz 1HL_5A_1.fq.gz 1HL_5A_2.fq.gz 1HL_6A_1.fq.gz 1HL_6A_2.fq.gz 1HL_7A_1.fq.gz 1HL_7A_2.fq.gz 1HL_8A_1.fq.gz 1HL_8A_2.fq.gz 1HL_9A_1.fq.gz 1HL_9A_2.fq.gz 1NF_10A_1.fq.gz 1NF_10A_2.fq.gz 1NF_11A_1.fq.gz 1NF_11A_2.fq.gz 1NF_12A_1.fq.gz 1NF_12A_2.fq.gz 1NF_13A_1.fq.gz 1NF_13A_2.fq.gz 1NF_14A_1.fq.gz 1NF_14A_2.fq.gz 1NF_15A_1.fq.gz 1NF_15A_2.fq.gz 1NF_16A_1.fq.gz 1NF_16A_2.fq.gz 1NF_17A_1.fq.gz 1NF_17A_2.fq.gz 1NF_18A_1.fq.gz 1NF_18A_2.fq.gz 1NF_19A_1.fq.gz 1NF_19A_2.fq.gz 1NF_1A_1.fq.gz 1NF_1A_2.fq.gz 1NF_20A_1.fq.gz 1NF_20A_2.fq.gz 1NF_21A_1.fq.gz 1NF_21A_2.fq.gz 1NF_22A_1.fq.gz 1NF_22A_2.fq.gz 1NF_23A_1.fq.gz 1NF_23A_2.fq.gz 1NF_24A_1.fq.gz 1NF_24A_2.fq.gz 1NF_25A_1.fq.gz 1NF_25A_2.fq.gz 1NF_26A_1.fq.gz 1NF_26A_2.fq.gz 1NF_27A_1.fq.gz 1NF_27A_2.fq.gz 1NF_28A_1.fq.gz 1NF_28A_2.fq.gz 1NF_29A_1.fq.gz 1NF_29A_2.fq.gz 1NF_2A_1.fq.gz 1NF_2A_2.fq.gz 1NF_30A_1.fq.gz 1NF_30A_2.fq.gz 1NF_31A_1.fq.gz 1NF_31A_2.fq.gz 1NF_32A_1.fq.gz 1NF_32A_2.fq.gz 1NF_33A_1.fq.gz 1NF_33A_2.fq.gz 1NF_4A_1.fq.gz 1NF_4A_2.fq.gz 1NF_5A_1.fq.gz 1NF_5A_2.fq.gz 1NF_6A_1.fq.gz 1NF_6A_2.fq.gz 1NF_7A_1.fq.gz 1NF_7A_2.fq.gz 1NF_8A_1.fq.gz 1NF_8A_2.fq.gz 1NF_9A_1.fq.gz 1NF_9A_2.fq.gz 1SN_10A_1.fq.gz 1SN_10A_2.fq.gz 1SN_11A_1.fq.gz 1SN_11A_2.fq.gz 1SN_12A_1.fq.gz 1SN_12A_2.fq.gz 1SN_13A_1.fq.gz 1SN_13A_2.fq.gz 1SN_14A_1.fq.gz 1SN_14A_2.fq.gz 1SN_15A_1.fq.gz 1SN_15A_2.fq.gz 1SN_16A_1.fq.gz 1SN_16A_2.fq.gz 1SN_17A_1.fq.gz 1SN_17A_2.fq.gz 1SN_18A_1.fq.gz 1SN_18A_2.fq.gz 1SN_19A_1.fq.gz 1SN_19A_2.fq.gz 1SN_1A_1.fq.gz 1SN_1A_2.fq.gz 1SN_20A_1.fq.gz 1SN_20A_2.fq.gz 1SN_21A_1.fq.gz 1SN_21A_2.fq.gz 1SN_22A_1.fq.gz 1SN_22A_2.fq.gz 1SN_23A_1.fq.gz 1SN_23A_2.fq.gz 1SN_24A_1.fq.gz 1SN_24A_2.fq.gz 1SN_25A_1.fq.gz 1SN_25A_2.fq.gz 1SN_26A_1.fq.gz 1SN_26A_2.fq.gz 1SN_27A_1.fq.gz 1SN_27A_2.fq.gz 1SN_28A_1.fq.gz 1SN_28A_2.fq.gz 1SN_29A_1.fq.gz 1SN_29A_2.fq.gz 1SN_2A_1.fq.gz 1SN_2A_2.fq.gz 1SN_30A_1.fq.gz 1SN_30A_2.fq.gz 1SN_31A_1.fq.gz 1SN_31A_2.fq.gz 1SN_32A_1.fq.gz 1SN_32A_2.fq.gz 1SN_3A_1.fq.gz 1SN_3A_2.fq.gz 1SN_4A_1.fq.gz 1SN_4A_2.fq.gz 1SN_5A_1.fq.gz 1SN_5A_2.fq.gz 1SN_6A_1.fq.gz 1SN_6A_2.fq.gz 1SN_7A_1.fq.gz 1SN_7A_2.fq.gz 1SN_8A_1.fq.gz 1SN_8A_2.fq.gz 1SN_9A_1.fq.gz 1SN_9A_2.fq.gz ' which didn't exist, or couldn't be read\n", "\n", "real\t0m0.203s\n", "user\t0m0.160s\n", "sys\t0m0.010s\n" ] } ], "source": [ "%%bash\n", "FASTQ_LIST=\"$(ls -1 *.gz| tr '\\n' ' ')\"\n", "time fastqc --extract --threads 96 --quiet \"$FASTQ_LIST\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Ha! The habit of always surrounding shell variables with quotations (to prevent elements in the variable that might contain spaces from screwing up a command) actually backfired! I WANT the spaces to be interepreted, because FastQC accepts a space-delimited list of filenames as input! By encasing the shell variable in quotes, FastQC viewed the entire list of files as a single input file!!" ] }, { "cell_type": "code", "execution_count": 33, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t327m47.227s\n", "user\t206m46.190s\n", "sys\t322m21.800s\n" ] } ], "source": [ "%%bash\n", "FASTQ_LIST=\"$(ls -1 *.gz| tr '\\n' ' ')\"\n", "time fastqc --extract --threads 96 --quiet $FASTQ_LIST" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let's see what was made. We'll ignore the gzipped FASTQ files using the ```--ignore``` argument." ] }, { "cell_type": "code", "execution_count": 34, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1HL_10A_1_fastqc\n", "1HL_10A_1_fastqc.html\n", "1HL_10A_1_fastqc.zip\n", "1HL_10A_2_fastqc\n", "1HL_10A_2_fastqc.html\n", "1HL_10A_2_fastqc.zip\n", "1HL_11A_1_fastqc\n", "1HL_11A_1_fastqc.html\n", "1HL_11A_1_fastqc.zip\n", "1HL_11A_2_fastqc\n", "1HL_11A_2_fastqc.html\n", "1HL_11A_2_fastqc.zip\n", "1HL_12A_1_fastqc\n", "1HL_12A_1_fastqc.html\n", "1HL_12A_1_fastqc.zip\n", "1HL_12A_2_fastqc\n", "1HL_12A_2_fastqc.html\n", "1HL_12A_2_fastqc.zip\n", "1HL_13A_1_fastqc\n", "1HL_13A_1_fastqc.html\n", "1HL_13A_1_fastqc.zip\n", "1HL_13A_2_fastqc\n", "1HL_13A_2_fastqc.html\n", "1HL_13A_2_fastqc.zip\n", "1HL_14A_1_fastqc\n", "1HL_14A_1_fastqc.html\n", "1HL_14A_1_fastqc.zip\n", "1HL_14A_2_fastqc\n", "1HL_14A_2_fastqc.html\n", "1HL_14A_2_fastqc.zip\n", "1HL_15A_1_fastqc\n", 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"1SN_6A_1_fastqc.zip\n", "1SN_6A_2_fastqc\n", "1SN_6A_2_fastqc.html\n", "1SN_6A_2_fastqc.zip\n", "1SN_7A_1_fastqc\n", "1SN_7A_1_fastqc.html\n", "1SN_7A_1_fastqc.zip\n", "1SN_7A_2_fastqc\n", "1SN_7A_2_fastqc.html\n", "1SN_7A_2_fastqc.zip\n", "1SN_8A_1_fastqc\n", "1SN_8A_1_fastqc.html\n", "1SN_8A_1_fastqc.zip\n", "1SN_8A_2_fastqc\n", "1SN_8A_2_fastqc.html\n", "1SN_8A_2_fastqc.zip\n", "1SN_9A_1_fastqc\n", "1SN_9A_1_fastqc.html\n", "1SN_9A_1_fastqc.zip\n", "1SN_9A_2_fastqc\n", "1SN_9A_2_fastqc.html\n", "1SN_9A_2_fastqc.zip\n", "outputtest.txt\n", "owl_checksums.md5\n", "temp_checksums.md5\n" ] } ], "source": [ "%%bash\n", "ls --ignore=\"*.gz\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Cool, fastqc output! Let's look in one of the folders to see what's doin'." ] }, { "cell_type": "code", "execution_count": 35, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0m\u001b[01;34mIcons\u001b[0m/ \u001b[01;34mImages\u001b[0m/ fastqc.fo fastqc_data.txt fastqc_report.html summary.txt\r\n" ] } ], "source": [ "ls 1SN_9A_1_fastqc/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let's make sure there's FastQC output for each input file (there should be 192 .zip files)" ] }, { "cell_type": "code", "execution_count": 36, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "192\r\n" ] } ], "source": [ "ls -1 *.zip | wc -l" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Move FastQC output folders to Owl.\n", "\n", "The ```-t``` specifies the target directory. I think this is needed so that each folder that is moved keeps the folder name, instead of just copying the contents within the folder to the destination..." ] }, { "cell_type": "code", "execution_count": 37, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t2m15.669s\n", "user\t0m0.030s\n", "sys\t0m13.490s\n" ] } ], "source": [ "%%bash\n", "time \\\n", "mv \\\n", "-t /owl_web/nightingales/O_lurida/20160223_gbs/ \\\n", "*fastqc/" ] }, { "cell_type": "code", "execution_count": 38, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1HL_10A_1_fastqc.html\n", "1HL_10A_1_fastqc.zip\n", "1HL_10A_2_fastqc.html\n", "1HL_10A_2_fastqc.zip\n", "1HL_11A_1_fastqc.html\n", "1HL_11A_1_fastqc.zip\n", "1HL_11A_2_fastqc.html\n", "1HL_11A_2_fastqc.zip\n", "1HL_12A_1_fastqc.html\n", "1HL_12A_1_fastqc.zip\n", "1HL_12A_2_fastqc.html\n", "1HL_12A_2_fastqc.zip\n", "1HL_13A_1_fastqc.html\n", 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--ignore=\"*.gz\"" ] }, { "cell_type": "code", "execution_count": 39, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc\n", "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc\n", "1HL_10A_1_fastqc\n", "1HL_10A_2_fastqc\n", "1HL_11A_1_fastqc\n", "1HL_11A_2_fastqc\n", "1HL_12A_1_fastqc\n", "1HL_12A_2_fastqc\n", "1HL_13A_1_fastqc\n", "1HL_13A_2_fastqc\n", "1HL_14A_1_fastqc\n", "1HL_14A_2_fastqc\n", "1HL_15A_1_fastqc\n", "1HL_15A_2_fastqc\n", "1HL_16A_1_fastqc\n", "1HL_16A_2_fastqc\n", "1HL_17A_1_fastqc\n", "1HL_17A_2_fastqc\n", "1HL_19A_1_fastqc\n", "1HL_19A_2_fastqc\n", "1HL_1A_1_fastqc\n", "1HL_1A_2_fastqc\n", "1HL_20A_1_fastqc\n", "1HL_20A_2_fastqc\n", "1HL_21A_1_fastqc\n", "1HL_21A_2_fastqc\n", "1HL_22A_1_fastqc\n", "1HL_22A_2_fastqc\n", "1HL_23A_1_fastqc\n", "1HL_23A_2_fastqc\n", "1HL_24A_1_fastqc\n", "1HL_24A_2_fastqc\n", "1HL_25A_1_fastqc\n", "1HL_25A_2_fastqc\n", "1HL_26A_1_fastqc\n", "1HL_26A_2_fastqc\n", "1HL_27A_1_fastqc\n", "1HL_27A_2_fastqc\n", "1HL_28A_1_fastqc\n", "1HL_28A_2_fastqc\n", "1HL_29A_1_fastqc\n", "1HL_29A_2_fastqc\n", "1HL_2A_1_fastqc\n", "1HL_2A_2_fastqc\n", "1HL_31A_1_fastqc\n", "1HL_31A_2_fastqc\n", "1HL_33A_1_fastqc\n", "1HL_33A_2_fastqc\n", "1HL_34A_1_fastqc\n", "1HL_34A_2_fastqc\n", "1HL_35A_1_fastqc\n", "1HL_35A_2_fastqc\n", "1HL_3A_1_fastqc\n", "1HL_3A_2_fastqc\n", "1HL_4A_1_fastqc\n", "1HL_4A_2_fastqc\n", "1HL_5A_1_fastqc\n", "1HL_5A_2_fastqc\n", "1HL_6A_1_fastqc\n", "1HL_6A_2_fastqc\n", "1HL_7A_1_fastqc\n", "1HL_7A_2_fastqc\n", "1HL_8A_1_fastqc\n", "1HL_8A_2_fastqc\n", "1HL_9A_1_fastqc\n", "1HL_9A_2_fastqc\n", "1NF_10A_1_fastqc\n", "1NF_10A_2_fastqc\n", "1NF_11A_1_fastqc\n", "1NF_11A_2_fastqc\n", "1NF_12A_1_fastqc\n", "1NF_12A_2_fastqc\n", "1NF_13A_1_fastqc\n", "1NF_13A_2_fastqc\n", "1NF_14A_1_fastqc\n", "1NF_14A_2_fastqc\n", "1NF_15A_1_fastqc\n", "1NF_15A_2_fastqc\n", "1NF_16A_1_fastqc\n", "1NF_16A_2_fastqc\n", "1NF_17A_1_fastqc\n", "1NF_17A_2_fastqc\n", "1NF_18A_1_fastqc\n", "1NF_18A_2_fastqc\n", "1NF_19A_1_fastqc\n", "1NF_19A_2_fastqc\n", "1NF_1A_1_fastqc\n", "1NF_1A_2_fastqc\n", "1NF_20A_1_fastqc\n", "1NF_20A_2_fastqc\n", "1NF_21A_1_fastqc\n", "1NF_21A_2_fastqc\n", "1NF_22A_1_fastqc\n", "1NF_22A_2_fastqc\n", "1NF_23A_1_fastqc\n", "1NF_23A_2_fastqc\n", "1NF_24A_1_fastqc\n", "1NF_24A_2_fastqc\n", "1NF_25A_1_fastqc\n", "1NF_25A_2_fastqc\n", "1NF_26A_1_fastqc\n", "1NF_26A_2_fastqc\n", "1NF_27A_1_fastqc\n", "1NF_27A_2_fastqc\n", "1NF_28A_1_fastqc\n", "1NF_28A_2_fastqc\n", "1NF_29A_1_fastqc\n", "1NF_29A_2_fastqc\n", "1NF_2A_1_fastqc\n", "1NF_2A_2_fastqc\n", "1NF_30A_1_fastqc\n", "1NF_30A_2_fastqc\n", "1NF_31A_1_fastqc\n", "1NF_31A_2_fastqc\n", "1NF_32A_1_fastqc\n", "1NF_32A_2_fastqc\n", "1NF_33A_1_fastqc\n", "1NF_33A_2_fastqc\n", "1NF_4A_1_fastqc\n", "1NF_4A_2_fastqc\n", "1NF_5A_1_fastqc\n", "1NF_5A_2_fastqc\n", "1NF_6A_1_fastqc\n", "1NF_6A_2_fastqc\n", "1NF_7A_1_fastqc\n", "1NF_7A_2_fastqc\n", "1NF_8A_1_fastqc\n", "1NF_8A_2_fastqc\n", "1NF_9A_1_fastqc\n", "1NF_9A_2_fastqc\n", "1SN_10A_1_fastqc\n", "1SN_10A_2_fastqc\n", "1SN_11A_1_fastqc\n", "1SN_11A_2_fastqc\n", "1SN_12A_1_fastqc\n", "1SN_12A_2_fastqc\n", "1SN_13A_1_fastqc\n", "1SN_13A_2_fastqc\n", "1SN_14A_1_fastqc\n", "1SN_14A_2_fastqc\n", "1SN_15A_1_fastqc\n", "1SN_15A_2_fastqc\n", "1SN_16A_1_fastqc\n", "1SN_16A_2_fastqc\n", "1SN_17A_1_fastqc\n", "1SN_17A_2_fastqc\n", "1SN_18A_1_fastqc\n", "1SN_18A_2_fastqc\n", "1SN_19A_1_fastqc\n", "1SN_19A_2_fastqc\n", "1SN_1A_1_fastqc\n", "1SN_1A_2_fastqc\n", "1SN_20A_1_fastqc\n", "1SN_20A_2_fastqc\n", "1SN_21A_1_fastqc\n", "1SN_21A_2_fastqc\n", "1SN_22A_1_fastqc\n", "1SN_22A_2_fastqc\n", "1SN_23A_1_fastqc\n", "1SN_23A_2_fastqc\n", "1SN_24A_1_fastqc\n", "1SN_24A_2_fastqc\n", "1SN_25A_1_fastqc\n", "1SN_25A_2_fastqc\n", "1SN_26A_1_fastqc\n", "1SN_26A_2_fastqc\n", "1SN_27A_1_fastqc\n", "1SN_27A_2_fastqc\n", "1SN_28A_1_fastqc\n", "1SN_28A_2_fastqc\n", "1SN_29A_1_fastqc\n", "1SN_29A_2_fastqc\n", "1SN_2A_1_fastqc\n", "1SN_2A_2_fastqc\n", "1SN_30A_1_fastqc\n", "1SN_30A_2_fastqc\n", "1SN_31A_1_fastqc\n", "1SN_31A_2_fastqc\n", "1SN_32A_1_fastqc\n", "1SN_32A_2_fastqc\n", "1SN_3A_1_fastqc\n", "1SN_3A_2_fastqc\n", "1SN_4A_1_fastqc\n", "1SN_4A_2_fastqc\n", "1SN_5A_1_fastqc\n", "1SN_5A_2_fastqc\n", "1SN_6A_1_fastqc\n", "1SN_6A_2_fastqc\n", "1SN_7A_1_fastqc\n", "1SN_7A_2_fastqc\n", "1SN_8A_1_fastqc\n", "1SN_8A_2_fastqc\n", "1SN_9A_1_fastqc\n", "1SN_9A_2_fastqc\n", "checksums.md5\n", "index.lst\n", "md5.check\n", "md5.txt\n", "md51.txt\n", "readme.md\n", "split.sh\n" ] } ], "source": [ "%%bash\n", "ls --ignore=\"*.gz\" /owl_web/nightingales/O_lurida/20160223_gbs/" ] }, { "cell_type": "code", "execution_count": 40, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Icons\n", "Images\n", "fastqc.fo\n", "fastqc_data.txt\n", "fastqc_report.html\n", "summary.txt\n" ] } ], "source": [ "%%bash\n", "ls /owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now, let's move the HTML files." ] }, { "cell_type": "code", "execution_count": 41, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv *.html /owl_web/nightingales/O_lurida/20160223_gbs/" ] }, { "cell_type": "code", "execution_count": 42, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_17A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_17A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_19A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_19A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_1A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_1A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_20A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_20A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_21A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_21A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_22A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_22A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_23A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_23A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_24A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_24A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_25A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_25A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_26A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_26A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_27A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_27A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_28A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_28A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_29A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_29A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_2A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_2A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_31A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_31A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_33A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_33A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_34A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_34A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1HL_35A_1_fastqc.html\n", 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"/owl_web/nightingales/O_lurida/20160223_gbs/1NF_29A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_2A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_2A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_30A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_30A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_31A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_31A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_32A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_32A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_33A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_33A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_4A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_4A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_5A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_5A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_6A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_6A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_7A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_7A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_8A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_8A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_9A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1NF_9A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_10A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_10A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_11A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_11A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_14A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_14A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_15A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_15A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_16A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_16A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_17A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_17A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_18A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_18A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_19A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_19A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_1A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_1A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html\n", "/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html\n" ] } ], "source": [ "%%bash\n", "ls /owl_web/nightingales/O_lurida/20160223_gbs/*.html" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Everything looks good! Let's get rid of the clutter we created on Ostrich for this analsysis." ] }, { "cell_type": "code", "execution_count": 43, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/data\n" ] } ], "source": [ "cd /data/" ] }, { "cell_type": "code", "execution_count": 44, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0m\u001b[01;34m20161117_oly_gbs_vcf_analysis\u001b[0m/ test_file10.txt.gz test_file7.txt.gz\r\n", "\u001b[01;34m20170227_jay_data_tmp\u001b[0m/ test_file2.txt.gz test_file8.txt.gz\r\n", "\u001b[01;34m20170301_fastqc_gbs\u001b[0m/ test_file3.txt.gz test_file9.txt.gz\r\n", "\u001b[01;34m20170306_fastqc_gbs\u001b[0m/ test_file4.txt.gz wgetrc_berk_seq\r\n", "md5s.txt test_file5.txt.gz\r\n", "test_file1.txt.gz test_file6.txt.gz\r\n" ] } ], "source": [ "ls" ] }, { "cell_type": "code", "execution_count": 45, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "rm -rf 20170306_fastqc_gbs/" ] }, { "cell_type": "code", "execution_count": 46, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0m\u001b[01;34m20161117_oly_gbs_vcf_analysis\u001b[0m/ test_file10.txt.gz test_file6.txt.gz\r\n", "\u001b[01;34m20170227_jay_data_tmp\u001b[0m/ test_file2.txt.gz test_file7.txt.gz\r\n", "\u001b[01;34m20170301_fastqc_gbs\u001b[0m/ test_file3.txt.gz test_file8.txt.gz\r\n", "md5s.txt test_file4.txt.gz test_file9.txt.gz\r\n", "test_file1.txt.gz test_file5.txt.gz wgetrc_berk_seq\r\n" ] } ], "source": [ "ls" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let's generate a list of markdown-formatted links for all of the HTML files." ] }, { "cell_type": "code", "execution_count": 47, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "bash: line 3: printf: - : invalid option\n", "printf: usage: printf [-v var] format [arguments]\n", "bash: line 3: printf: - : invalid option\n", "printf: usage: printf [-v var] format [arguments]\n", "bash: line 3: printf: - : invalid option\n", "printf: usage: printf [-v var] format [arguments]\n", "bash: line 3: printf: - : invalid option\n", "printf: usage: printf [-v var] format [arguments]\n", "bash: line 3: printf: - : invalid option\n", "printf: usage: printf [-v var] format [arguments]\n", "bash: line 3: printf: - : invalid option\n", "printf: usage: printf [-v var] format [arguments]\n", "bash: line 3: printf: - : invalid option\n", "printf: usage: printf [-v var] format [arguments]\n", "bash: line 3: printf: - : invalid option\n", "printf: usage: printf [-v var] format [arguments]\n", "bash: line 3: printf: - : invalid option\n", "printf: usage: printf [-v var] format [arguments]\n", "bash: line 3: printf: - : invalid option\n", "printf: usage: printf [-v var] format [arguments]\n", "bash: line 3: printf: - 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: invalid option\n", "printf: usage: printf [-v var] format [arguments]\n", "bash: line 3: printf: - : invalid option\n", "printf: usage: printf [-v var] format [arguments]\n" ] } ], "source": [ "%%bash\n", "for html in /owl_web/nightingales/O_lurida/20160223_gbs/1[1HNS]*.html\n", " do\n", " printf \"- [%s](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/%s)\" \"$html\" \"$html\"\n", " done" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Well, the hyphen caused an issue. Let's try to escape the hyphen so it's not interpreted as an option indicator." ] }, { "cell_type": "code", "execution_count": 48, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc.html)\\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_2_fastqc.html)\\- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_1_fastqc.html)\\- 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[/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html)\\- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html)\\- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html)\\- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html)\\- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html)" ] } ], "source": [ "%%bash\n", "for html in /owl_web/nightingales/O_lurida/20160223_gbs/1[1HNS]*.html\n", " do\n", " printf \"\\- [%s](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/%s)\" \"$html\" \"$html\"\n", " done" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "That didn't work, as the backslash is interpreted literally.\n", "\n", "I'm doing this incorrectly. I should be specifying the print format and then providing printf with the junk I want printed...\n", "\n", "The code below tells printf to print four strings in a row, followed by a newline. The %s indicates a string should printed in this position. The list of possible strings (each item in the list is contained in quotes and separated from other items by a space) is supplied after the format layout. The list is \"consumed\" in order (i.e. The first %s uses the first string in the list. 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[/owl_web/nightingales/O_lurida/20160223_gbs/1SN_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_11A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_14A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_14A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_15A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_15A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_16A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_16A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_17A_1_fastqc.html\n", "- 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[/owl_web/nightingales/O_lurida/20160223_gbs/1SN_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_19A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_1A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_1A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs//owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html\n" ] } ], "source": [ "%%bash\n", "for html in /owl_web/nightingales/O_lurida/20160223_gbs/1[1HNS]*.html\n", " do\n", " printf \"%s%s%s%s\\n\" \"- \" \"[$html]\" \"(http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\" \"$html\"\n", " done" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Closer... But, it turns out that the for loop is storing the entire path for each file in the ```html``` variable. I only want the file name.\n", "\n", "The command below uses parameter substitution (```${html##*/}```)to delete the path from the value stored in the ```html``` variable (i.e. it deletes everything before, and including, the last forward slash from the value stored in the ```html``` variable)." ] }, { "cell_type": "code", "execution_count": 50, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_10A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_11A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_11A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_12A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_12A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_13A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_13A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_14A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_14A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_15A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_15A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_16A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_16A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_17A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_17A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_19A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_19A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_1A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_1A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_20A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_20A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_21A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_21A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_22A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_22A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_23A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_23A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_24A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_24A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_25A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_25A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_26A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_26A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_27A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_27A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_28A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_28A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_29A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_29A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_2A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_2A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_31A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_31A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_33A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_33A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_33A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_33A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_34A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_34A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_34A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_34A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_35A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_35A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_35A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_35A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_3A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_3A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_3A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_3A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_4A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_4A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_5A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_5A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_6A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_6A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_7A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_7A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_8A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_8A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_9A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_9A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_10A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_10A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_11A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_11A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_12A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_12A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_13A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_13A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_14A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_14A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_15A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_15A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_16A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_16A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_17A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_17A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_18A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_18A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_18A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_18A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_19A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_19A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_1A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_1A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_20A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_20A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_21A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_21A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_22A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_22A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_23A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_23A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_24A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_24A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_25A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_25A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_26A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_26A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_27A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_27A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_28A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_28A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_29A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_29A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_2A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_2A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_30A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_30A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_30A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_30A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_31A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_31A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_32A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_32A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_32A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_32A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_33A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_33A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_33A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_33A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_4A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_4A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_5A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_5A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_6A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_6A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_7A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_7A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_8A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_8A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_9A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_9A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_10A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_10A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_11A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_11A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_12A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_12A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_13A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_13A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_14A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_14A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_15A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_15A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_16A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_16A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_17A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_17A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_18A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_18A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_18A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_18A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_19A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_19A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_1A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_1A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_20A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_20A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_21A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_21A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_22A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_22A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_23A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_23A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_24A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_24A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_25A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_25A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_26A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_26A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_27A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_27A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_28A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_28A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_29A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_29A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_2A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_2A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_30A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_30A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_30A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_31A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_31A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_32A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_32A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_32A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_3A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_3A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_3A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_4A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_4A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_5A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_5A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_6A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_6A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_7A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html\n", ")\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html\n", ")\n" ] } ], "source": [ "%%bash\n", "for html in /owl_web/nightingales/O_lurida/20160223_gbs/1[1HNS]*.html\n", " do\n", " printf \"%s%s%s%s\\n\" \\\n", " \"- \" \"[$html]\" \"(http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\" \"${html##*/}\" \")\"\n", " done" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Much closer... But, I forgot to add an additional %s to the printf format to account for the addition of the \")\" that I added to the list of strings." ] }, { "cell_type": "code", "execution_count": 51, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_10A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_10A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_11A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_11A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_12A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_12A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_13A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_13A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_14A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_14A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_15A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_15A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_16A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_16A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_17A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_17A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_19A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_19A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_1A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_1A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_20A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_20A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_21A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_21A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_22A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_22A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_23A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1HL_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1HL_23A_2_fastqc.html)\n", "- 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[/owl_web/nightingales/O_lurida/20160223_gbs/1NF_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_10A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_10A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_11A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_11A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_12A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_12A_2_fastqc.html)\n", "- 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[/owl_web/nightingales/O_lurida/20160223_gbs/1NF_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_16A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_16A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_17A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_17A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_18A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_18A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_18A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_18A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_19A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_19A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_1A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_1A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_20A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_20A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_21A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_21A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_22A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_22A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_23A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_23A_2_fastqc.html)\n", "- 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[/owl_web/nightingales/O_lurida/20160223_gbs/1NF_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_27A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_27A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_28A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_28A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_29A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1NF_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1NF_29A_2_fastqc.html)\n", "- 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[/owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_6A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_6A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_7A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_7A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_8A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_8A_2_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_9A_1_fastqc.html)\n", "- [/owl_web/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/1SN_9A_2_fastqc.html)\n" ] } ], "source": [ "%%bash\n", "for html in /owl_web/nightingales/O_lurida/20160223_gbs/1[1HNS]*.html\n", " do\n", " printf \"%s%s%s%s%s\\n\" \\\n", " \"- \" \"[$html]\" \"(http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\" \"${html##*/}\" \")\"\n", " done" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "OMG! So, so close. I want the output to just display the filename for the link; not the full file path. Put another parameter substitution and this should work the way I wanted..." ] }, { "cell_type": "code", "execution_count": 52, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "- [1HL_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_10A_1_fastqc.html)\n", "- [1HL_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_10A_2_fastqc.html)\n", "- [1HL_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_11A_1_fastqc.html)\n", "- [1HL_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_11A_2_fastqc.html)\n", "- [1HL_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_12A_1_fastqc.html)\n", "- [1HL_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_12A_2_fastqc.html)\n", "- 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"1NF_11A_2_fastqc.html)\n", "- [1NF_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_12A_1_fastqc.html)\n", "- [1NF_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_12A_2_fastqc.html)\n", "- [1NF_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_13A_1_fastqc.html)\n", "- [1NF_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_13A_2_fastqc.html)\n", "- [1NF_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_14A_1_fastqc.html)\n", "- [1NF_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_14A_2_fastqc.html)\n", "- [1NF_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_15A_1_fastqc.html)\n", "- [1NF_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_15A_2_fastqc.html)\n", "- [1NF_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_16A_1_fastqc.html)\n", "- [1NF_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_16A_2_fastqc.html)\n", "- [1NF_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_17A_1_fastqc.html)\n", "- [1NF_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_17A_2_fastqc.html)\n", "- [1NF_18A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_18A_1_fastqc.html)\n", "- [1NF_18A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_18A_2_fastqc.html)\n", "- [1NF_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_19A_1_fastqc.html)\n", "- [1NF_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_19A_2_fastqc.html)\n", "- [1NF_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_1A_1_fastqc.html)\n", "- [1NF_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_1A_2_fastqc.html)\n", "- [1NF_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_20A_1_fastqc.html)\n", "- [1NF_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_20A_2_fastqc.html)\n", "- [1NF_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_21A_1_fastqc.html)\n", "- [1NF_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_21A_2_fastqc.html)\n", "- [1NF_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_22A_1_fastqc.html)\n", "- [1NF_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_22A_2_fastqc.html)\n", "- [1NF_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_23A_1_fastqc.html)\n", "- [1NF_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_23A_2_fastqc.html)\n", "- [1NF_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_24A_1_fastqc.html)\n", "- [1NF_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_24A_2_fastqc.html)\n", "- [1NF_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_25A_1_fastqc.html)\n", "- [1NF_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_25A_2_fastqc.html)\n", "- [1NF_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_26A_1_fastqc.html)\n", "- [1NF_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_26A_2_fastqc.html)\n", "- [1NF_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_27A_1_fastqc.html)\n", "- [1NF_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_27A_2_fastqc.html)\n", "- [1NF_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_28A_1_fastqc.html)\n", "- [1NF_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_28A_2_fastqc.html)\n", "- [1NF_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_29A_1_fastqc.html)\n", "- [1NF_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_29A_2_fastqc.html)\n", "- [1NF_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_2A_1_fastqc.html)\n", "- [1NF_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_2A_2_fastqc.html)\n", "- [1NF_30A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_30A_1_fastqc.html)\n", "- [1NF_30A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_30A_2_fastqc.html)\n", "- [1NF_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_31A_1_fastqc.html)\n", "- [1NF_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_31A_2_fastqc.html)\n", "- [1NF_32A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_32A_1_fastqc.html)\n", "- [1NF_32A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_32A_2_fastqc.html)\n", "- [1NF_33A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_33A_1_fastqc.html)\n", "- [1NF_33A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_33A_2_fastqc.html)\n", "- [1NF_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_4A_1_fastqc.html)\n", "- [1NF_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_4A_2_fastqc.html)\n", "- [1NF_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_5A_1_fastqc.html)\n", "- [1NF_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_5A_2_fastqc.html)\n", "- [1NF_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_6A_1_fastqc.html)\n", "- [1NF_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_6A_2_fastqc.html)\n", "- [1NF_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_7A_1_fastqc.html)\n", "- [1NF_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_7A_2_fastqc.html)\n", "- [1NF_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_8A_1_fastqc.html)\n", "- [1NF_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_8A_2_fastqc.html)\n", "- [1NF_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_9A_1_fastqc.html)\n", "- [1NF_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_9A_2_fastqc.html)\n", "- [1SN_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_10A_1_fastqc.html)\n", "- [1SN_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_10A_2_fastqc.html)\n", "- [1SN_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_11A_1_fastqc.html)\n", "- [1SN_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_11A_2_fastqc.html)\n", "- [1SN_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_12A_1_fastqc.html)\n", "- [1SN_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_12A_2_fastqc.html)\n", "- [1SN_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_13A_1_fastqc.html)\n", "- [1SN_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_13A_2_fastqc.html)\n", "- [1SN_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_14A_1_fastqc.html)\n", "- [1SN_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_14A_2_fastqc.html)\n", "- [1SN_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_15A_1_fastqc.html)\n", "- [1SN_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_15A_2_fastqc.html)\n", "- [1SN_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_16A_1_fastqc.html)\n", "- [1SN_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_16A_2_fastqc.html)\n", "- [1SN_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_17A_1_fastqc.html)\n", "- [1SN_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_17A_2_fastqc.html)\n", "- [1SN_18A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_18A_1_fastqc.html)\n", "- [1SN_18A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_18A_2_fastqc.html)\n", "- [1SN_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_19A_1_fastqc.html)\n", "- [1SN_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_19A_2_fastqc.html)\n", "- [1SN_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_1A_1_fastqc.html)\n", "- [1SN_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_1A_2_fastqc.html)\n", "- [1SN_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_20A_1_fastqc.html)\n", "- [1SN_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_20A_2_fastqc.html)\n", "- [1SN_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_21A_1_fastqc.html)\n", "- [1SN_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_21A_2_fastqc.html)\n", "- [1SN_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_22A_1_fastqc.html)\n", "- [1SN_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_22A_2_fastqc.html)\n", "- [1SN_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_23A_1_fastqc.html)\n", "- [1SN_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_23A_2_fastqc.html)\n", "- [1SN_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_24A_1_fastqc.html)\n", "- [1SN_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_24A_2_fastqc.html)\n", "- [1SN_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_25A_1_fastqc.html)\n", "- [1SN_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_25A_2_fastqc.html)\n", "- [1SN_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_26A_1_fastqc.html)\n", "- [1SN_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_26A_2_fastqc.html)\n", "- [1SN_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_27A_1_fastqc.html)\n", "- [1SN_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_27A_2_fastqc.html)\n", "- [1SN_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_28A_1_fastqc.html)\n", "- [1SN_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_28A_2_fastqc.html)\n", "- [1SN_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_29A_1_fastqc.html)\n", "- [1SN_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_29A_2_fastqc.html)\n", "- [1SN_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_2A_1_fastqc.html)\n", "- [1SN_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_2A_2_fastqc.html)\n", "- [1SN_30A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_30A_1_fastqc.html)\n", "- [1SN_30A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_30A_2_fastqc.html)\n", "- [1SN_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_31A_1_fastqc.html)\n", "- [1SN_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_31A_2_fastqc.html)\n", "- [1SN_32A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_32A_1_fastqc.html)\n", "- [1SN_32A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_32A_2_fastqc.html)\n", "- [1SN_3A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_3A_1_fastqc.html)\n", "- [1SN_3A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_3A_2_fastqc.html)\n", "- [1SN_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_4A_1_fastqc.html)\n", "- [1SN_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_4A_2_fastqc.html)\n", "- [1SN_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_5A_1_fastqc.html)\n", "- [1SN_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_5A_2_fastqc.html)\n", "- [1SN_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_6A_1_fastqc.html)\n", "- [1SN_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_6A_2_fastqc.html)\n", "- [1SN_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_7A_1_fastqc.html)\n", "- [1SN_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_7A_2_fastqc.html)\n", "- [1SN_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_8A_1_fastqc.html)\n", "- [1SN_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_8A_2_fastqc.html)\n", "- [1SN_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_9A_1_fastqc.html)\n", "- [1SN_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_9A_2_fastqc.html)\n" ] } ], "source": [ "%%bash\n", "for html in /owl_web/nightingales/O_lurida/20160223_gbs/1[1HNS]*.html\n", " do\n", " printf \"%s%s%s%s%s\\n\" \\\n", " \"- \" \"[\" \"\"${html##*/}\"\" \"]\" \"(http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\" \"${html##*/}\" \")\"\n", " done" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "At last! Here are the links to all of the FastQC reports!\n", "\n", "- [1HL_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_10A_1_fastqc.html)\n", "- [1HL_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_10A_2_fastqc.html)\n", "- [1HL_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_11A_1_fastqc.html)\n", "- [1HL_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_11A_2_fastqc.html)\n", "- [1HL_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_12A_1_fastqc.html)\n", "- [1HL_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_12A_2_fastqc.html)\n", "- [1HL_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_13A_1_fastqc.html)\n", "- [1HL_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_13A_2_fastqc.html)\n", "- [1HL_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_14A_1_fastqc.html)\n", "- [1HL_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_14A_2_fastqc.html)\n", "- [1HL_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_15A_1_fastqc.html)\n", "- [1HL_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_15A_2_fastqc.html)\n", "- [1HL_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_16A_1_fastqc.html)\n", "- [1HL_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_16A_2_fastqc.html)\n", "- [1HL_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_17A_1_fastqc.html)\n", "- [1HL_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_17A_2_fastqc.html)\n", "- [1HL_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_19A_1_fastqc.html)\n", "- [1HL_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_19A_2_fastqc.html)\n", "- [1HL_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_1A_1_fastqc.html)\n", "- [1HL_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_1A_2_fastqc.html)\n", "- [1HL_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_20A_1_fastqc.html)\n", "- [1HL_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_20A_2_fastqc.html)\n", "- [1HL_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_21A_1_fastqc.html)\n", "- [1HL_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_21A_2_fastqc.html)\n", "- [1HL_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_22A_1_fastqc.html)\n", "- [1HL_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_22A_2_fastqc.html)\n", "- [1HL_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_23A_1_fastqc.html)\n", "- [1HL_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_23A_2_fastqc.html)\n", "- [1HL_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_24A_1_fastqc.html)\n", "- [1HL_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_24A_2_fastqc.html)\n", "- [1HL_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_25A_1_fastqc.html)\n", "- [1HL_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_25A_2_fastqc.html)\n", "- [1HL_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_26A_1_fastqc.html)\n", "- [1HL_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_26A_2_fastqc.html)\n", "- [1HL_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_27A_1_fastqc.html)\n", "- [1HL_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_27A_2_fastqc.html)\n", "- [1HL_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_28A_1_fastqc.html)\n", "- [1HL_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_28A_2_fastqc.html)\n", "- [1HL_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_29A_1_fastqc.html)\n", "- [1HL_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_29A_2_fastqc.html)\n", "- [1HL_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_2A_1_fastqc.html)\n", "- [1HL_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_2A_2_fastqc.html)\n", "- [1HL_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_31A_1_fastqc.html)\n", "- [1HL_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_31A_2_fastqc.html)\n", "- [1HL_33A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_33A_1_fastqc.html)\n", "- [1HL_33A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_33A_2_fastqc.html)\n", "- [1HL_34A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_34A_1_fastqc.html)\n", "- [1HL_34A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_34A_2_fastqc.html)\n", "- [1HL_35A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_35A_1_fastqc.html)\n", "- [1HL_35A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_35A_2_fastqc.html)\n", "- [1HL_3A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_3A_1_fastqc.html)\n", "- [1HL_3A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_3A_2_fastqc.html)\n", "- [1HL_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_4A_1_fastqc.html)\n", "- [1HL_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_4A_2_fastqc.html)\n", "- [1HL_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_5A_1_fastqc.html)\n", "- [1HL_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_5A_2_fastqc.html)\n", "- [1HL_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_6A_1_fastqc.html)\n", "- [1HL_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_6A_2_fastqc.html)\n", "- [1HL_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_7A_1_fastqc.html)\n", "- [1HL_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_7A_2_fastqc.html)\n", "- [1HL_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_8A_1_fastqc.html)\n", "- [1HL_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_8A_2_fastqc.html)\n", "- [1HL_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_9A_1_fastqc.html)\n", "- [1HL_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1HL_9A_2_fastqc.html)\n", "- [1NF_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_10A_1_fastqc.html)\n", "- [1NF_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_10A_2_fastqc.html)\n", "- [1NF_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_11A_1_fastqc.html)\n", "- [1NF_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_11A_2_fastqc.html)\n", "- [1NF_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_12A_1_fastqc.html)\n", "- [1NF_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_12A_2_fastqc.html)\n", "- [1NF_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_13A_1_fastqc.html)\n", "- [1NF_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_13A_2_fastqc.html)\n", "- [1NF_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_14A_1_fastqc.html)\n", "- [1NF_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_14A_2_fastqc.html)\n", "- [1NF_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_15A_1_fastqc.html)\n", "- [1NF_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_15A_2_fastqc.html)\n", "- [1NF_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_16A_1_fastqc.html)\n", "- [1NF_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_16A_2_fastqc.html)\n", "- [1NF_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_17A_1_fastqc.html)\n", "- [1NF_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_17A_2_fastqc.html)\n", "- [1NF_18A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_18A_1_fastqc.html)\n", "- [1NF_18A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_18A_2_fastqc.html)\n", "- [1NF_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_19A_1_fastqc.html)\n", "- [1NF_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_19A_2_fastqc.html)\n", "- [1NF_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_1A_1_fastqc.html)\n", "- [1NF_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_1A_2_fastqc.html)\n", "- [1NF_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_20A_1_fastqc.html)\n", "- [1NF_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_20A_2_fastqc.html)\n", "- [1NF_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_21A_1_fastqc.html)\n", "- [1NF_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_21A_2_fastqc.html)\n", "- [1NF_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_22A_1_fastqc.html)\n", "- [1NF_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_22A_2_fastqc.html)\n", "- [1NF_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_23A_1_fastqc.html)\n", "- [1NF_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_23A_2_fastqc.html)\n", "- [1NF_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_24A_1_fastqc.html)\n", "- [1NF_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_24A_2_fastqc.html)\n", "- [1NF_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_25A_1_fastqc.html)\n", "- [1NF_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_25A_2_fastqc.html)\n", "- [1NF_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_26A_1_fastqc.html)\n", "- [1NF_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_26A_2_fastqc.html)\n", "- [1NF_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_27A_1_fastqc.html)\n", "- [1NF_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_27A_2_fastqc.html)\n", "- [1NF_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_28A_1_fastqc.html)\n", "- [1NF_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_28A_2_fastqc.html)\n", "- [1NF_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_29A_1_fastqc.html)\n", "- [1NF_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_29A_2_fastqc.html)\n", "- [1NF_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_2A_1_fastqc.html)\n", "- [1NF_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_2A_2_fastqc.html)\n", "- [1NF_30A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_30A_1_fastqc.html)\n", "- [1NF_30A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_30A_2_fastqc.html)\n", "- [1NF_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_31A_1_fastqc.html)\n", "- [1NF_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_31A_2_fastqc.html)\n", "- [1NF_32A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_32A_1_fastqc.html)\n", "- [1NF_32A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_32A_2_fastqc.html)\n", "- [1NF_33A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_33A_1_fastqc.html)\n", "- [1NF_33A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_33A_2_fastqc.html)\n", "- [1NF_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_4A_1_fastqc.html)\n", "- [1NF_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_4A_2_fastqc.html)\n", "- [1NF_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_5A_1_fastqc.html)\n", "- [1NF_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_5A_2_fastqc.html)\n", "- [1NF_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_6A_1_fastqc.html)\n", "- [1NF_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_6A_2_fastqc.html)\n", "- [1NF_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_7A_1_fastqc.html)\n", "- [1NF_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_7A_2_fastqc.html)\n", "- [1NF_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_8A_1_fastqc.html)\n", "- [1NF_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_8A_2_fastqc.html)\n", "- [1NF_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_9A_1_fastqc.html)\n", "- [1NF_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1NF_9A_2_fastqc.html)\n", "- [1SN_10A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_10A_1_fastqc.html)\n", "- [1SN_10A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_10A_2_fastqc.html)\n", "- [1SN_11A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_11A_1_fastqc.html)\n", "- [1SN_11A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_11A_2_fastqc.html)\n", "- [1SN_12A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_12A_1_fastqc.html)\n", "- [1SN_12A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_12A_2_fastqc.html)\n", "- [1SN_13A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_13A_1_fastqc.html)\n", "- [1SN_13A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_13A_2_fastqc.html)\n", "- [1SN_14A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_14A_1_fastqc.html)\n", "- [1SN_14A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_14A_2_fastqc.html)\n", "- [1SN_15A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_15A_1_fastqc.html)\n", "- [1SN_15A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_15A_2_fastqc.html)\n", "- [1SN_16A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_16A_1_fastqc.html)\n", "- [1SN_16A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_16A_2_fastqc.html)\n", "- [1SN_17A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_17A_1_fastqc.html)\n", "- [1SN_17A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_17A_2_fastqc.html)\n", "- [1SN_18A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_18A_1_fastqc.html)\n", "- [1SN_18A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_18A_2_fastqc.html)\n", "- [1SN_19A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_19A_1_fastqc.html)\n", "- [1SN_19A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_19A_2_fastqc.html)\n", "- [1SN_1A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_1A_1_fastqc.html)\n", "- [1SN_1A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_1A_2_fastqc.html)\n", "- [1SN_20A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_20A_1_fastqc.html)\n", "- [1SN_20A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_20A_2_fastqc.html)\n", "- [1SN_21A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_21A_1_fastqc.html)\n", "- [1SN_21A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_21A_2_fastqc.html)\n", "- [1SN_22A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_22A_1_fastqc.html)\n", "- [1SN_22A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_22A_2_fastqc.html)\n", "- [1SN_23A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_23A_1_fastqc.html)\n", "- [1SN_23A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_23A_2_fastqc.html)\n", "- [1SN_24A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_24A_1_fastqc.html)\n", "- [1SN_24A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_24A_2_fastqc.html)\n", "- [1SN_25A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_25A_1_fastqc.html)\n", "- [1SN_25A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_25A_2_fastqc.html)\n", "- [1SN_26A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_26A_1_fastqc.html)\n", "- [1SN_26A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_26A_2_fastqc.html)\n", "- [1SN_27A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_27A_1_fastqc.html)\n", "- [1SN_27A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_27A_2_fastqc.html)\n", "- [1SN_28A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_28A_1_fastqc.html)\n", "- [1SN_28A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_28A_2_fastqc.html)\n", "- [1SN_29A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_29A_1_fastqc.html)\n", "- [1SN_29A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_29A_2_fastqc.html)\n", "- [1SN_2A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_2A_1_fastqc.html)\n", "- [1SN_2A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_2A_2_fastqc.html)\n", "- [1SN_30A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_30A_1_fastqc.html)\n", "- [1SN_30A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_30A_2_fastqc.html)\n", "- [1SN_31A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_31A_1_fastqc.html)\n", "- [1SN_31A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_31A_2_fastqc.html)\n", "- [1SN_32A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_32A_1_fastqc.html)\n", "- [1SN_32A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_32A_2_fastqc.html)\n", "- [1SN_3A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_3A_1_fastqc.html)\n", "- [1SN_3A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_3A_2_fastqc.html)\n", "- [1SN_4A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_4A_1_fastqc.html)\n", "- [1SN_4A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_4A_2_fastqc.html)\n", "- [1SN_5A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_5A_1_fastqc.html)\n", "- [1SN_5A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_5A_2_fastqc.html)\n", "- [1SN_6A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_6A_1_fastqc.html)\n", "- [1SN_6A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_6A_2_fastqc.html)\n", "- [1SN_7A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_7A_1_fastqc.html)\n", "- [1SN_7A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_7A_2_fastqc.html)\n", "- [1SN_8A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_8A_1_fastqc.html)\n", "- [1SN_8A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_8A_2_fastqc.html)\n", "- [1SN_9A_1_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_9A_1_fastqc.html)\n", "- [1SN_9A_2_fastqc.html](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/\n", "1SN_9A_2_fastqc.html)" ] } ], 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