{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "### Methylation analysis of Olympia oyster BSseq data using Bismark\n", "\n", "#### Note: The two initial steps of the Bismark pipeline had the output cells stripped due to extremely verbose output, leading to a very large file size for the notebook (it was virtually unviewable)." ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mkdir /home/sam/analyses/20180709_oly_methylseq" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Run Bismark\n", "\n", "Genome preparation had previously been run:\n", "\n", "[Notebook 20180508](http://onsnetwork.org/kubu4/2018/05/08/bs-seq-mapping-olympia-oyster-bisulfite-sequencing-trimgalore-fastqc-bismark/)\n", "\n", "---\n", "\n", "The following command completed in 19,756 minutes (or, 13.7 days)!" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "time \\\n", "/home/shared/Bismark-0.19.1/bismark \\\n", "--path_to_bowtie /home/shared/bowtie2-2.3.4.1-linux-x86_64/ \\\n", "--genome /home/sam/data/oly_methylseq/20180503_oly_genome_pbjelly_sjw_01_bismark \\\n", "-p 16 \\\n", "--non_directional \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/1_ATCACG_L001_R1_001_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/2_CGATGT_L001_R1_001_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/3_TTAGGC_L001_R1_001_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/4_TGACCA_L001_R1_001_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/5_ACAGTG_L001_R1_001_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/6_GCCAAT_L001_R1_001_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/7_CAGATC_L001_R1_001_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/8_ACTTGA_L001_R1_001_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_10_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_11_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_12_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_13_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_14_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_15_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_16_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_17_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_18_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_1_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_2_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_3_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_4_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_5_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_6_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_7_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_8_s456_trimmed.fq.gz \\\n", "/home/sam/analyses/20180503_oly_methylseq_trimgalore/zr1394_9_s456_trimmed.fq.gz \\\n", "1> /home/sam/analyses/20180709_oly_methylseq/20180709_bismark_01.out\n", "2> /home/sam/analyses/20180709_oly_methylseq/20180709_bismark_01.err" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [ "sed '/^Subject:/ s/ / bismark JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "ls" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Didn't switch directories. Need to move files to desired analyis directory." ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 21G\n", "-rw-rw-r-- 1 sam sam 239M Jul 9 13:14 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 9 13:14 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 0 Jul 23 03:25 20180709_bismark_01.err\n", "-rw-rw-r-- 1 sam sam 18M Jul 23 03:25 20180709_bismark_01.out\n", "-rw-rw-r-- 1 sam sam 296M Jul 9 17:05 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 9 17:05 2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 295M Jul 9 20:52 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 9 20:52 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 293M Jul 10 00:39 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 00:39 4_TGACCA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 310M Jul 10 04:40 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 04:40 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 307M Jul 10 08:39 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 08:39 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 258M Jul 10 12:00 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 12:00 7_CAGATC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 351M Jul 10 16:34 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 16:34 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.5G Jul 11 15:33 zr1394_10_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 11 15:33 zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 901M Jul 12 06:54 zr1394_11_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 12 06:55 zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.2G Jul 13 00:37 zr1394_12_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 13 00:37 zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.1G Jul 13 19:08 zr1394_13_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 13 19:08 zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.5G Jul 14 20:01 zr1394_14_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 14 20:01 zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.2G Jul 15 15:12 zr1394_15_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 15 15:13 zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.2G Jul 16 12:12 zr1394_16_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 16 12:12 zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 740M Jul 17 00:19 zr1394_17_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 17 00:19 zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.1G Jul 17 16:42 zr1394_18_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 17 16:42 zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 829M Jul 18 06:19 zr1394_1_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 18 06:19 zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 843M Jul 18 19:50 zr1394_2_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 18 19:50 zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 842M Jul 19 09:46 zr1394_3_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 19 09:46 zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 793M Jul 19 22:46 zr1394_4_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 19 22:46 zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 892M Jul 20 12:53 zr1394_5_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 20 12:53 zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 879M Jul 21 02:44 zr1394_6_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 21 02:44 zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 878M Jul 21 17:06 zr1394_7_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 21 17:06 zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 690M Jul 22 04:21 zr1394_8_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 22 04:21 zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.4G Jul 23 03:25 zr1394_9_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 23 03:25 zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "mv: cannot stat '*bt2*': No such file or directory\n" ] } ], "source": [ "%%bash\n", "mv *bt2* /home/sam/analyses/20180709_oly_methylseq/\n", "ls -lh /home/sam/analyses/20180709_oly_methylseq/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Deduplication" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t132m33.812s\n", "user\t254m16.060s\n", "sys\t4m15.860s\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/analyses/20180709_oly_methylseq/\n", "time \\\n", "/home/shared/Bismark-0.19.1/deduplicate_bismark \\\n", "--bam \\\n", "--single \\\n", "*.bam \\\n", "1> 20180805_dedup.out \\\n", "2> 20180805_dedup.err\n", "sed '/^Subject:/ s/ / deduplication JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 35G\n", "-rw-rw-r-- 1 sam sam 239M Jul 9 13:14 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 213M Aug 6 12:59 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 12:59 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 9 13:14 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 0 Jul 23 03:25 20180709_bismark_01.err\n", "-rw-rw-r-- 1 sam sam 18M Jul 23 03:25 20180709_bismark_01.out\n", "-rw-rw-r-- 1 sam sam 16K Aug 6 15:10 20180805_dedup.err\n", "-rw-rw-r-- 1 sam sam 849M Aug 6 15:10 20180805_dedup.out\n", "-rw-rw-r-- 1 sam sam 296M Jul 9 17:05 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 261M Aug 6 13:01 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 13:01 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 9 17:05 2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 295M Jul 9 20:52 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 259M Aug 6 13:03 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 13:03 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 9 20:52 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 293M Jul 10 00:39 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 260M Aug 6 13:05 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 13:05 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 00:39 4_TGACCA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 310M Jul 10 04:40 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 271M Aug 6 13:08 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 13:08 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 04:40 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 307M Jul 10 08:39 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 270M Aug 6 13:10 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 13:10 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 08:39 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 258M Jul 10 12:00 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 233M Aug 6 13:12 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 13:12 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 12:00 7_CAGATC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 351M Jul 10 16:34 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 307M Aug 6 13:14 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 13:14 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 16:34 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.5G Jul 11 15:33 zr1394_10_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 520M Aug 6 13:23 zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 294 Aug 6 13:23 zr1394_10_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 11 15:33 zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 901M Jul 12 06:54 zr1394_11_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 478M Aug 6 13:28 zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 293 Aug 6 13:28 zr1394_11_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 12 06:55 zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.2G Jul 13 00:37 zr1394_12_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 776M Aug 6 13:36 zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 294 Aug 6 13:36 zr1394_12_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 13 00:37 zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.1G Jul 13 19:08 zr1394_13_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 648M Aug 6 13:42 zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 294 Aug 6 13:42 zr1394_13_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 13 19:08 zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.5G Jul 14 20:01 zr1394_14_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 829M Aug 6 13:51 zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 295 Aug 6 13:51 zr1394_14_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 14 20:01 zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.2G Jul 15 15:12 zr1394_15_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 626M Aug 6 13:58 zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 294 Aug 6 13:58 zr1394_15_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 15 15:13 zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.2G Jul 16 12:12 zr1394_16_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 690M Aug 6 14:05 zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 294 Aug 6 14:05 zr1394_16_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 16 12:12 zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 740M Jul 17 00:19 zr1394_17_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 457M Aug 6 14:09 zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 293 Aug 6 14:09 zr1394_17_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 17 00:19 zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.1G Jul 17 16:42 zr1394_18_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 690M Aug 6 14:16 zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 294 Aug 6 14:16 zr1394_18_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 17 16:42 zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 829M Jul 18 06:19 zr1394_1_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 588M Aug 6 14:21 zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 293 Aug 6 14:21 zr1394_1_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 18 06:19 zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 843M Jul 18 19:50 zr1394_2_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 591M Aug 6 14:27 zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 293 Aug 6 14:27 zr1394_2_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 18 19:50 zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 842M Jul 19 09:46 zr1394_3_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 601M Aug 6 14:33 zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 293 Aug 6 14:33 zr1394_3_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 19 09:46 zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 793M Jul 19 22:46 zr1394_4_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 550M Aug 6 14:38 zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 292 Aug 6 14:38 zr1394_4_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 19 22:46 zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 892M Jul 20 12:53 zr1394_5_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 673M Aug 6 14:44 zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 293 Aug 6 14:44 zr1394_5_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 20 12:53 zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 879M Jul 21 02:44 zr1394_6_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 674M Aug 6 14:50 zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 293 Aug 6 14:50 zr1394_6_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 21 02:44 zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 878M Jul 21 17:06 zr1394_7_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 617M Aug 6 14:56 zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 293 Aug 6 14:56 zr1394_7_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 21 17:06 zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 690M Jul 22 04:21 zr1394_8_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 491M Aug 6 15:01 zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 292 Aug 6 15:01 zr1394_8_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 22 04:21 zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.4G Jul 23 03:25 zr1394_9_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 945M Aug 6 15:10 zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 293 Aug 6 15:10 zr1394_9_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 23 03:25 zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/analyses/20180709_oly_methylseq/\n", "ls -lh" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Methylation extraction" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t120m22.874s\n", "user\t911m12.688s\n", "sys\t191m7.556s\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/analyses/20180709_oly_methylseq/\n", "time \\\n", "/home/shared/Bismark-0.19.1/bismark_methylation_extractor \\\n", "--bedgraph \\\n", "--counts \\\n", "--scaffolds \\\n", "--remove_spaces \\\n", "--multicore 16 \\\n", "--buffer_size 75% \\\n", "*deduplicated.bam \\\n", "1> 20180806_methyl_extraction.out \\\n", "2> 20180806_methyl_extraction.err\n", "sed '/^Subject:/ s/ / methyl extraction JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Bismark Processing Report" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t0m0.897s\n", "user\t0m0.404s\n", "sys\t0m0.096s\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/analyses/20180709_oly_methylseq/\n", "time \\\n", "/home/shared/Bismark-0.19.1/bismark2report \\\n", "1>20180813_bismark2report.out \\\n", "2>20180813_bismark2report.err\n", "sed '/^Subject:/ s/ / bismark2report JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "-rw-rw-r-- 1 sam sam 353734 Aug 13 15:02 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353746 Aug 13 15:02 2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353742 Aug 13 15:02 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353743 Aug 13 15:02 4_TGACCA_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353765 Aug 13 15:02 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353768 Aug 13 15:02 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353736 Aug 13 15:02 7_CAGATC_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353769 Aug 13 15:02 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353853 Aug 13 15:02 zr1394_10_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353845 Aug 13 15:02 zr1394_11_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353821 Aug 13 15:02 zr1394_12_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353828 Aug 13 15:02 zr1394_13_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353831 Aug 13 15:02 zr1394_14_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353848 Aug 13 15:02 zr1394_15_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353845 Aug 13 15:02 zr1394_16_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353837 Aug 13 15:02 zr1394_17_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353821 Aug 13 15:02 zr1394_18_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353820 Aug 13 15:02 zr1394_1_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353823 Aug 13 15:02 zr1394_2_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353820 Aug 13 15:02 zr1394_3_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353820 Aug 13 15:02 zr1394_4_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353819 Aug 13 15:02 zr1394_5_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353818 Aug 13 15:02 zr1394_6_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353820 Aug 13 15:02 zr1394_7_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353822 Aug 13 15:02 zr1394_9_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 353816 Aug 13 15:02 zr1394_8_s456_trimmed_bismark_bt2_SE_report.html\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/analyses/20180709_oly_methylseq/\n", "ls -ltr *.html" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Bismark summary report" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t0m0.090s\n", "user\t0m0.052s\n", "sys\t0m0.004s\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/analyses/20180709_oly_methylseq/\n", "time \\\n", "/home/shared/Bismark-0.19.1/bismark2summary \\\n", "1>20180813_bismark2summary.out \\\n", "2>20180813_bismark2summary.err\n", "sed '/^Subject:/ s/ / bismark2summary JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 154G\n", "-rw-rw-r-- 1 sam sam 239M Jul 9 13:14 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 9 13:14 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 296M Jul 9 17:05 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 9 17:05 2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 295M Jul 9 20:52 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 9 20:52 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 293M Jul 10 00:39 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 00:39 4_TGACCA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 310M Jul 10 04:40 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 04:40 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 307M Jul 10 08:39 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 08:39 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 258M Jul 10 12:00 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 12:00 7_CAGATC_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 351M Jul 10 16:34 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 10 16:34 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.5G Jul 11 15:33 zr1394_10_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 11 15:33 zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 901M Jul 12 06:54 zr1394_11_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 12 06:55 zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.2G Jul 13 00:37 zr1394_12_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 13 00:37 zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.1G Jul 13 19:08 zr1394_13_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 13 19:08 zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.5G Jul 14 20:01 zr1394_14_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 14 20:01 zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.2G Jul 15 15:12 zr1394_15_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 15 15:13 zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.2G Jul 16 12:12 zr1394_16_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 16 12:12 zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 740M Jul 17 00:19 zr1394_17_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 17 00:19 zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.1G Jul 17 16:42 zr1394_18_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 17 16:42 zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 829M Jul 18 06:19 zr1394_1_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 18 06:19 zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 843M Jul 18 19:50 zr1394_2_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 18 19:50 zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 842M Jul 19 09:46 zr1394_3_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 19 09:46 zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 793M Jul 19 22:46 zr1394_4_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 19 22:46 zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 892M Jul 20 12:53 zr1394_5_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 20 12:53 zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 879M Jul 21 02:44 zr1394_6_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 21 02:44 zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 878M Jul 21 17:06 zr1394_7_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 21 17:06 zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 690M Jul 22 04:21 zr1394_8_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 22 04:21 zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 1.4G Jul 23 03:25 zr1394_9_s456_trimmed_bismark_bt2.bam\n", "-rw-rw-r-- 1 sam sam 1.8K Jul 23 03:25 zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt\n", "-rw-rw-r-- 1 sam sam 18M Jul 23 03:25 20180709_bismark_01.out\n", "-rw-rw-r-- 1 sam sam 0 Jul 23 03:25 20180709_bismark_01.err\n", "-rw-rw-r-- 1 sam sam 213M Aug 6 12:59 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 12:59 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 261M Aug 6 13:01 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 13:01 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 259M Aug 6 13:03 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 13:03 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 260M Aug 6 13:05 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 13:05 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 271M Aug 6 13:08 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 13:08 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 270M Aug 6 13:10 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 13:10 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "-rw-rw-r-- 1 sam sam 233M Aug 6 13:12 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "-rw-rw-r-- 1 sam sam 296 Aug 6 13:12 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1 sam sam 161M Aug 6 17:30 CpG_OT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt\n", "-rw-rw-r-- 1 sam sam 143M Aug 6 17:30 CpG_CTOT_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt\n", "-rw-rw-r-- 1 sam sam 142M Aug 6 17:30 CpG_CTOB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt\n", "-rw-rw-r-- 1 sam sam 160M Aug 6 17:30 CpG_OB_zr1394_8_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt\n", "-rw-rw-r-- 1 sam sam 18M Aug 6 17:31 zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 18M Aug 6 17:31 zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz\n", "-rw-rw-r-- 1 sam sam 210M Aug 6 17:36 CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt\n", "-rw-rw-r-- 1 sam sam 210M Aug 6 17:36 CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt\n", "-rw-rw-r-- 1 sam sam 1.4G Aug 6 17:36 CHH_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt\n", "-rw-rw-r-- 1 sam sam 1.2G Aug 6 17:36 CHH_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt\n", "-rw-rw-r-- 1 sam sam 1.2G Aug 6 17:36 CHH_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt\n", "-rw-rw-r-- 1 sam sam 320M Aug 6 17:36 CHG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt\n", "-rw-rw-r-- 1 sam sam 319M Aug 6 17:36 CHG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt\n", "-rw-rw-r-- 1 sam sam 268M Aug 6 17:36 CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt\n", "-rw-rw-r-- 1 sam sam 267M Aug 6 17:36 CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt\n", "-rw-rw-r-- 1 sam sam 1.4G Aug 6 17:36 CHH_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt\n", "-rw-rw-r-- 1 sam sam 390M Aug 6 17:36 CHG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt\n", "-rw-rw-r-- 1 sam sam 390M Aug 6 17:36 CHG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt\n", "-rw-rw-r-- 1 sam sam 826 Aug 6 17:36 zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt\n", "-rw-rw-r-- 1 sam sam 3.0K Aug 6 17:36 zr1394_9_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt\n", "-rw-rw-r-- 1 sam sam 73K Aug 6 17:36 20180806_methyl_extraction.out\n", "-rw-rw-r-- 1 sam sam 268M Aug 6 17:37 CpG_OT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt\n", "-rw-rw-r-- 1 sam sam 210M Aug 6 17:37 CpG_CTOT_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt\n", "-rw-rw-r-- 1 sam sam 210M Aug 6 17:37 CpG_CTOB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt\n", "-rw-rw-r-- 1 sam sam 267M Aug 6 17:37 CpG_OB_zr1394_9_s456_trimmed_bismark_bt2.deduplicated.txt.spaces_removed.txt\n", "-rw-rw-r-- 1 sam sam 26M Aug 6 17:39 zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 27M Aug 6 17:39 zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz\n", "-rw-rw-r-- 1 sam sam 919M Aug 6 17:39 20180806_methyl_extraction.err\n", "-rw-rw-r-- 1 sam sam 0 Aug 13 15:02 20180813_bismark2report.out\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 4_TGACCA_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 7_CAGATC_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_10_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_11_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_12_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_13_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_14_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_15_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_16_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_17_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_18_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_1_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_2_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_3_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_4_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_5_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_6_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_7_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_9_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 346K Aug 13 15:02 zr1394_8_s456_trimmed_bismark_bt2_SE_report.html\n", "-rw-rw-r-- 1 sam sam 33K Aug 13 15:02 20180813_bismark2report.err\n", "-rw-rw-r-- 1 sam sam 0 Aug 13 15:05 20180813_bismark2summary.out\n", "-rw-rw-r-- 1 sam sam 4.2K Aug 13 15:05 bismark_summary_report.txt\n", "-rw-rw-r-- 1 sam sam 269K Aug 13 15:05 bismark_summary_report.html\n", "-rw-rw-r-- 1 sam sam 2.5K Aug 13 15:05 20180813_bismark2summary.err\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/analyses/20180709_oly_methylseq/\n", "ls -ltrh" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Folder copied to owl outside of notebook, due to ```sudo``` usage" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam\n", "1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bedGraph.gz\n", "1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bismark.cov.gz\n", "1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.M-bias.txt\n", "1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated_splitting_report.txt\n", "1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "1_ATCACG_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "20180709_bismark_01.err\n", "20180709_bismark_01.out\n", "20180805_dedup.err\n", "20180805_dedup.out\n", "20180806_methyl_extraction.err\n", "20180806_methyl_extraction.out\n", "20180813_bismark2report.err\n", "20180813_bismark2report.out\n", "20180813_bismark2summary.err\n", "20180813_bismark2summary.out\n", "2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam\n", "2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", "2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bedGraph.gz\n", "2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bismark.cov.gz\n", "2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.M-bias.txt\n", "2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated_splitting_report.txt\n", "2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplication_report.txt\n", "2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.html\n", "2_CGATGT_L001_R1_001_trimmed_bismark_bt2_SE_report.txt\n", "3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam\n", "3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam\n", 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"zr1394_17_s456_trimmed_bismark_bt2_SE_report.html\n", "zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt\n", "zr1394_18_s456_trimmed_bismark_bt2.bam\n", "zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam\n", "zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz\n", "zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz\n", "zr1394_18_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt\n", "zr1394_18_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt\n", "zr1394_18_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "zr1394_18_s456_trimmed_bismark_bt2_SE_report.html\n", "zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt\n", "zr1394_1_s456_trimmed_bismark_bt2.bam\n", "zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam\n", "zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz\n", "zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz\n", "zr1394_1_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt\n", "zr1394_1_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt\n", "zr1394_1_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "zr1394_1_s456_trimmed_bismark_bt2_SE_report.html\n", "zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt\n", "zr1394_2_s456_trimmed_bismark_bt2.bam\n", "zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam\n", "zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz\n", "zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz\n", "zr1394_2_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt\n", "zr1394_2_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt\n", "zr1394_2_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "zr1394_2_s456_trimmed_bismark_bt2_SE_report.html\n", "zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt\n", "zr1394_3_s456_trimmed_bismark_bt2.bam\n", "zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam\n", "zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz\n", "zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz\n", "zr1394_3_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt\n", "zr1394_3_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt\n", "zr1394_3_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "zr1394_3_s456_trimmed_bismark_bt2_SE_report.html\n", "zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt\n", "zr1394_4_s456_trimmed_bismark_bt2.bam\n", "zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam\n", "zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz\n", "zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz\n", "zr1394_4_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt\n", "zr1394_4_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt\n", "zr1394_4_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "zr1394_4_s456_trimmed_bismark_bt2_SE_report.html\n", "zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt\n", "zr1394_5_s456_trimmed_bismark_bt2.bam\n", "zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam\n", "zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz\n", "zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz\n", "zr1394_5_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt\n", "zr1394_5_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt\n", "zr1394_5_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "zr1394_5_s456_trimmed_bismark_bt2_SE_report.html\n", "zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt\n", "zr1394_6_s456_trimmed_bismark_bt2.bam\n", "zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam\n", "zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz\n", "zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz\n", "zr1394_6_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt\n", "zr1394_6_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt\n", "zr1394_6_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "zr1394_6_s456_trimmed_bismark_bt2_SE_report.html\n", "zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt\n", "zr1394_7_s456_trimmed_bismark_bt2.bam\n", "zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam\n", "zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz\n", "zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz\n", "zr1394_7_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt\n", "zr1394_7_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt\n", "zr1394_7_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "zr1394_7_s456_trimmed_bismark_bt2_SE_report.html\n", "zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt\n", "zr1394_8_s456_trimmed_bismark_bt2.bam\n", "zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam\n", "zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz\n", "zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz\n", "zr1394_8_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt\n", "zr1394_8_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt\n", "zr1394_8_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "zr1394_8_s456_trimmed_bismark_bt2_SE_report.html\n", "zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt\n", "zr1394_9_s456_trimmed_bismark_bt2.bam\n", "zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam\n", "zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bedGraph.gz\n", "zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bismark.cov.gz\n", "zr1394_9_s456_trimmed_bismark_bt2.deduplicated.M-bias.txt\n", "zr1394_9_s456_trimmed_bismark_bt2.deduplicated_splitting_report.txt\n", "zr1394_9_s456_trimmed_bismark_bt2.deduplication_report.txt\n", "zr1394_9_s456_trimmed_bismark_bt2_SE_report.html\n", "zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt\n" ] } ], "source": [ "%%bash\n", "ls /mnt/owl/Athaliana/20180709_oly_methylseq/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Sort files for methylkit and IGV\n", "\n", "Used incorrect naming, so re-ran.\n", "\n", "Then, killed after realizing I could set thread count to speed things up." ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "[bam_sort_core] merging from 0 files and 16 in-memory blocks...\n", "\n", "real\t14m48.065s\n", "user\t177m2.984s\n", "sys\t1m58.888s\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/analyses/20180709_oly_methylseq\n", "time \\\n", "find *deduplicated.bam | \\\n", "xargs basename -s .bam | \\\n", "xargs -I{} /home/shared/samtools-1.8/samtools \\\n", "sort --threads 16 {}.bam \\\n", "-o {}.sorted.bam\n", "sed '/^Subject:/ s/ / sorting JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_10_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_11_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_12_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_13_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_14_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_15_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_16_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_17_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_18_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_1_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_2_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_3_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_4_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_5_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_6_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_7_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_8_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "zr1394_9_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/analyses/20180709_oly_methylseq\n", "ls *sorted*" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Indexing sorted files for IGV\n", "\n", "The \"```-@ 16```\" below specifies number of CPU threads to use." ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "cd /home/sam/analyses/20180709_oly_methylseq\n", "find *.sorted.bam | \\\n", "xargs basename -s .sorted.bam | \\\n", "xargs -I{} /home/shared/samtools-1.8/samtools \\\n", "index -@ 16 {}.sorted.bam\n", "sed '/^Subject:/ s/ / indexing JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_10_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_11_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_12_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_13_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_14_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_15_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_16_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_17_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_18_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_1_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_2_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_3_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_4_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_5_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_6_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_7_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_8_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "zr1394_9_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/analyses/20180709_oly_methylseq\n", "ls *.bai" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Copied files to owl outside of notebook due to ```sudo``` requirement" ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "-rw-rw-r-- 1 sam users 209M Aug 16 09:49 /mnt/owl/Athaliana/20180709_oly_methylseq/1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 27M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 254M Aug 16 09:49 /mnt/owl/Athaliana/20180709_oly_methylseq/2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 28M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 252M Aug 16 09:49 /mnt/owl/Athaliana/20180709_oly_methylseq/3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 28M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 254M Aug 16 09:50 /mnt/owl/Athaliana/20180709_oly_methylseq/4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 28M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 264M Aug 16 09:50 /mnt/owl/Athaliana/20180709_oly_methylseq/5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 28M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 263M Aug 16 09:50 /mnt/owl/Athaliana/20180709_oly_methylseq/6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 28M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 227M Aug 16 09:51 /mnt/owl/Athaliana/20180709_oly_methylseq/7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 27M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 298M Aug 16 09:51 /mnt/owl/Athaliana/20180709_oly_methylseq/8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 29M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 454M Aug 16 09:51 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_10_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 28M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_10_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 419M Aug 16 09:52 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_11_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 28M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_11_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 693M Aug 16 09:53 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_12_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 31M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_12_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 565M Aug 16 09:53 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_13_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 29M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_13_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 723M Aug 16 09:54 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_14_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 32M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_14_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 542M Aug 16 09:55 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_15_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 29M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_15_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 600M Aug 16 09:56 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_16_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 30M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_16_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 400M Aug 16 09:56 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_17_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 26M Aug 16 10:17 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_17_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 611M Aug 16 09:57 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_18_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 30M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_18_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 529M Aug 16 09:58 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_1_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 30M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_1_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 533M Aug 16 09:58 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_2_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 29M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_2_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 543M Aug 16 09:59 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_3_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 30M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_3_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 492M Aug 16 10:00 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_4_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 28M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_4_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 613M Aug 16 10:00 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_5_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 32M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_5_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 617M Aug 16 10:01 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_6_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 31M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_6_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 551M Aug 16 10:02 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_7_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 29M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_7_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 440M Aug 16 10:02 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_8_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 27M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_8_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n", "-rw-rw-r-- 1 sam users 840M Aug 16 10:03 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_9_s456_trimmed_bismark_bt2.deduplicated.sorted.bam\n", "-rw-rw-r-- 1 sam users 33M Aug 16 10:18 /mnt/owl/Athaliana/20180709_oly_methylseq/zr1394_9_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.bai\n" ] } ], "source": [ "%%bash\n", "ls -lh /mnt/owl/Athaliana/20180709_oly_methylseq/*sorted*" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 2", "language": "python", "name": "python2" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.12" } }, "nbformat": 4, "nbformat_minor": 2 }