{ "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": [ "Wed Mar 1 20:13:26 UTC 2017\n" ] } ], "source": [ "%%bash\n", "date" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Check computer specs" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "0f2bca9c664b\n" ] } ], "source": [ "%%bash\n", "hostname" ] }, { "cell_type": "code", "execution_count": 3, "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 non-demultiplexed BGI FASTQ files to local computer (Ostrich) and verfiy checksums" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "\u001b[0m\u001b[01;32m1HL_10A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1HL_10A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1HL_11A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1HL_11A_2.fq.gz\u001b[0m*\n", 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"\u001b[01;32m1SN_15A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_15A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_16A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_16A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_17A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_17A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_18A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_18A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_19A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_19A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_1A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_1A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_20A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_20A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_21A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_21A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_22A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_22A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_23A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_23A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_24A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_24A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_25A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_25A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_26A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_26A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_27A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_27A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_28A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_28A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_29A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_29A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_2A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_2A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_30A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_30A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_31A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_31A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_32A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_32A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_3A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_3A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_4A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_4A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_5A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_5A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_6A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_6A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_7A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_7A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_8A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_8A_2.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_9A_1.fq.gz\u001b[0m*\n", "\u001b[01;32m1SN_9A_2.fq.gz\u001b[0m*\n", "\u001b[01;32mUnKnow_1.fq.gz\u001b[0m*\n", "\u001b[01;32mUnKnow_2.fq.gz\u001b[0m*\n", "\u001b[01;32mbgi_project_summary.tar.gz\u001b[0m*\n", "checksums.md5\n", "index.lst\n", "\u001b[01;32mmd5.check\u001b[0m*\n", "\u001b[01;32mmd5.txt\u001b[0m*\n", "md51.txt\n", "readme.md\n", "split.sh\n" ] } ], "source": [ "ls /owl_web/nightingales/O_lurida/20160223_gbs/" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mkdir /data/20170301_fastqc_gbs" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/data/20170301_fastqc_gbs\n" ] } ], "source": [ "cd /data/20170301_fastqc_gbs/" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t31m9.816s\n", "user\t0m0.020s\n", "sys\t5m31.590s\n" ] } ], "source": [ "%%bash\n", "time for file in /owl_web/nightingales/O_lurida/20160223_gbs/160123*\n", " do\n", " cp \"$file\" .\n", " done" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Generate MD5 checksums & compare to original checksums" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "bash: line 3: md5: command not found\n", "bash: line 3: md5: command not found\n", "\n", "real\t0m0.020s\n", "user\t0m0.010s\n", "sys\t0m0.000s\n" ] } ], "source": [ "%%bash\n", "time for file in *.gz\n", " do\n", " md5 \"$file\" >> temp_checksums.md5\n", " done" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "cat temp_checksums.md5_checksums.md5" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 37G\n", "-rw-r--r-- 1 srlab staff 17G Mar 1 20:36 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "-rw-r--r-- 1 srlab staff 20G Mar 1 20:54 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "-rw-r--r-- 1 srlab staff 0 Mar 1 20:54 temp_checksums.md5\n" ] } ], "source": [ "%%bash\n", "ls -lh" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Whoops! Typos in both of the above commands. Will re-run..." ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t7m1.077s\n", "user\t0m3.950s\n", "sys\t4m11.280s\n" ] } ], "source": [ "%%bash\n", "time for file in *.gz\n", " do\n", " md5sum \"$file\" >> temp_checksums.md5\n", " done" ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "afd18614b9f5694af1a59672821cd0db 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "2894dd9b54c1388d3d74e8f8642aa267 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n" ] } ], "source": [ "%%bash\n", "cat temp_checksums.md5" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "awk: line 1: syntax error at or near [\n" ] } ], "source": [ "%%bash\n", "awk '/160123_I132/[print $0]' /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Bracket typo. Redo..." ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "MD5 (/Volumes/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz) = afd18614b9f5694af1a59672821cd0db\n", "MD5 (/Volumes/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz) = 2894dd9b54c1388d3d74e8f8642aa267\n" ] } ], "source": [ "%%bash\n", "awk '/160123_I132/{print $0}' /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Visual comparison looks good. Will proceed with FastQC" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### FastQC Analysis" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/usr/local/bioinformatics/FastQC/fastqc\n" ] } ], "source": [ "%%bash\n", "which fastqc" ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Analysis complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Analysis complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started analysis of 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 5% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 10% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 15% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 20% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 25% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 30% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 35% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 40% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 45% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 50% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 55% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 60% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 65% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 70% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 75% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 80% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 85% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 90% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Approx 95% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\n", "Started analysis of 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 5% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 10% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 15% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 20% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 25% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 30% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 35% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 40% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 45% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 50% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 55% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 60% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 65% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 70% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 75% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 80% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 85% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 90% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "Approx 95% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\n", "\n", "real\t353m56.148s\n", "user\t28m26.990s\n", "sys\t215m31.450s\n" ] } ], "source": [ "%%bash\n", "time fastqc --extract 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz" ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 37G\r\n", "-rw-r--r-- 1 srlab staff 17G Mar 1 20:36 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "drwxr-xr-x 1 srlab staff 272 Mar 2 00:35 \u001b[0m\u001b[01;34m160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc\u001b[0m/\r\n", "-rw-r--r-- 1 srlab staff 294K Mar 2 00:35 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc.html\r\n", "-rw-r--r-- 1 srlab staff 403K Mar 2 00:35 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc.zip\r\n", "-rw-r--r-- 1 srlab staff 20G Mar 1 20:54 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "drwxr-xr-x 1 srlab staff 272 Mar 2 03:12 \u001b[01;34m160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc\u001b[0m/\r\n", "-rw-r--r-- 1 srlab staff 347K Mar 2 03:12 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc.html\r\n", "-rw-r--r-- 1 srlab staff 489K Mar 2 03:12 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc.zip\r\n", "-rw-r--r-- 1 srlab staff 186 Mar 1 21:10 temp_checksums.md5\r\n" ] } ], "source": [ "ls -lh" ] }, { "cell_type": "code", "execution_count": 20, "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 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "PASS\tBasic Statistics\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "PASS\tPer base sequence quality\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "WARN\tPer tile sequence quality\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "PASS\tPer sequence quality scores\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "WARN\tPer base sequence content\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "PASS\tPer sequence GC content\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "PASS\tPer base N content\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "PASS\tSequence Length Distribution\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "FAIL\tSequence Duplication Levels\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "PASS\tOverrepresented sequences\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "FAIL\tAdapter Content\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "FAIL\tKmer Content\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n" ] } ], "source": [ "cat 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/summary.txt" ] }, { "cell_type": "code", "execution_count": 22, "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 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/" ] }, { "cell_type": "code", "execution_count": 23, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "cat: 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/: Is a directory\r\n" ] } ], "source": [ "cat 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/s" ] }, { "cell_type": "code", "execution_count": 24, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "PASS\tBasic Statistics\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "FAIL\tPer base sequence quality\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "FAIL\tPer tile sequence quality\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "PASS\tPer sequence quality scores\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "FAIL\tPer base sequence content\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "PASS\tPer sequence GC content\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "WARN\tPer base N content\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "PASS\tSequence Length Distribution\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "FAIL\tSequence Duplication Levels\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "WARN\tOverrepresented sequences\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "FAIL\tAdapter Content\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "FAIL\tKmer Content\t160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n" ] } ], "source": [ "cat 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/summary.txt" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Move the FastQC Outputs to Nightingales" ] }, { "cell_type": "code", "execution_count": 25, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc.fo' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc.fo'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc_data.txt' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc_data.txt'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc_report.html' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc_report.html'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/error.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/error.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/fastqc_icon.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/fastqc_icon.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/tick.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/tick.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/warning.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/warning.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/adapter_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/adapter_content.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/duplication_levels.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/duplication_levels.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/kmer_profiles.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/kmer_profiles.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_n_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_n_content.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_quality.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_quality.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_sequence_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_sequence_content.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_sequence_gc_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_sequence_gc_content.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_sequence_quality.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_sequence_quality.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_tile_quality.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_tile_quality.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/sequence_length_distribution.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/sequence_length_distribution.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/summary.txt' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/summary.txt'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc.fo'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc_data.txt'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc_report.html'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/error.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/fastqc_icon.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/tick.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/warning.png'\n", "removed directory: '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/adapter_content.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/duplication_levels.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/kmer_profiles.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_n_content.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_quality.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_sequence_content.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_sequence_gc_content.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_sequence_quality.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_tile_quality.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/sequence_length_distribution.png'\n", "removed directory: '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/summary.txt'\n", "removed directory: '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc.fo' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc.fo'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc_data.txt' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc_data.txt'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc_report.html' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc_report.html'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/error.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/error.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/fastqc_icon.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/fastqc_icon.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/tick.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/tick.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/warning.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/warning.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/adapter_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/adapter_content.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/duplication_levels.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/duplication_levels.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/kmer_profiles.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/kmer_profiles.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_n_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_n_content.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_quality.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_quality.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_sequence_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_sequence_content.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_sequence_gc_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_sequence_gc_content.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_sequence_quality.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_sequence_quality.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_tile_quality.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_tile_quality.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/sequence_length_distribution.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/sequence_length_distribution.png'\n", "'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/summary.txt' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/summary.txt'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc.fo'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc_data.txt'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc_report.html'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/error.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/fastqc_icon.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/tick.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/warning.png'\n", "removed directory: '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/adapter_content.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/duplication_levels.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/kmer_profiles.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_n_content.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_quality.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_sequence_content.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_sequence_gc_content.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_sequence_quality.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_tile_quality.png'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/sequence_length_distribution.png'\n", "removed directory: '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images'\n", "removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/summary.txt'\n", "removed directory: '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/'\n" ] } ], "source": [ "%%bash\n", "mv -v 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/ \\\n", "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/ \\\n", "-t /owl_web/nightingales/O_lurida/20160223_gbs/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### View FastQC Reports\n", "\n", "Easier viewing can be had by visiting the two folling links:\n", "\n", "- [20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc_report.html)\n", "\n", "- [20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc](http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc_report.html)" ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "%%HTML\n", "" ] }, { "cell_type": "code", "execution_count": 28, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "%%HTML\n", "" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "These results aren't terribly surprising since these data haven't been quality trimmed to remove adapter/barcode sequences." ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/data/20170301_fastqc_gbs\n" ] } ], "source": [ "cd /data/20170301_fastqc_gbs/" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc.html\r\n", "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc.zip\r\n", "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc.html\r\n", "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc.zip\r\n", "temp_checksums.md5\r\n" ] } ], "source": [ "ls" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Forgot to move the .html files!" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv *.html /owl_web/nightingales/O_lurida/20160223_gbs/" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz\r\n", "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc.zip\r\n", "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz\r\n", "160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc.zip\r\n", "temp_checksums.md5\r\n" ] } ], "source": [ "ls" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Clean up." ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/data\n" ] } ], "source": [ "cd /data/" ] }, { "cell_type": "code", "execution_count": 6, "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": "code", "execution_count": 7, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "rm -rf 20170301_fastqc_gbs/" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[0m\u001b[01;34m20161117_oly_gbs_vcf_analysis\u001b[0m/ test_file2.txt.gz test_file7.txt.gz\r\n", "\u001b[01;34m20170227_jay_data_tmp\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", "test_file10.txt.gz test_file6.txt.gz\r\n" ] } ], "source": [ "ls" ] } ], "metadata": { "anaconda-cloud": {}, "kernelspec": { "display_name": "Python [default]", "language": "python", "name": "python2" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, 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