{ "metadata": { "name": "", "signature": "sha256:cd1c48e107b0cf29347434460e381cf2b8d515810e230cc0f868e318be85c510" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "Workflow for processing BSseq Data" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This example will use _C gigas_ larvae data." ] }, { "cell_type": "code", "collapsed": false, "input": [ "#Setting Variables\n", "R1=\"filtered_Y38_control_GTGAAA_L005_R1\"\n", "R2=\"filtered_Y38_control_GTGAAA_L005_R2\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 6 }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "File extraction" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/{R1}.fastq.gz" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 13 }, { "cell_type": "code", "collapsed": false, "input": [ "!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/{R2}.fastq.gz" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 14 }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Quality Check (local)" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!/Volumes/Bay3/Software/FastQC/fastqc \\\n", "/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/{R1}.fastq \\\n", "-o /Volumes/web/cnidarian/" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Started analysis of filtered_Y38_control_GTGAAA_L005_R1.fastq\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Approx 5% complete for filtered_Y38_control_GTGAAA_L005_R1.fastq\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Approx 10% complete for filtered_Y38_control_GTGAAA_L005_R1.fastq\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Approx 15% complete for 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90% complete for filtered_Y38_control_GTGAAA_L005_R1.fastq\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Approx 95% complete for filtered_Y38_control_GTGAAA_L005_R1.fastq\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Approx 100% complete for filtered_Y38_control_GTGAAA_L005_R1.fastq\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Analysis complete for filtered_Y38_control_GTGAAA_L005_R1.fastq\r\n" ] } ], "prompt_number": 15 }, { "cell_type": "code", "collapsed": false, "input": [ "!/Volumes/Bay3/Software/FastQC/fastqc \\\n", "/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/{R2}.fastq \\\n", "-q \\\n", "-o /Volumes/web/cnidarian/" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 16 }, { "cell_type": "markdown", "metadata": {}, "source": [ "" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!grep -A 5 \"Overrepresented\" /Volumes/web/cnidarian/{R1}_fastqc/fastqc_data.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">>Overrepresented sequences\tfail\r\n", "#Sequence\tCount\tPercentage\tPossible Source\r\n", "GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTG\t77030\t2.233517550930463\tTruSeq Adapter, Index 1 (97% over 35bp)\r\n", ">>END_MODULE\r\n", ">>Kmer Content\tfail\r\n", "#Sequence\tCount\tObs/Exp Overall\tObs/Exp Max\tMax Obs/Exp Position\r\n" ] } ], "prompt_number": 17 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep -A 6 \"Overrepresented\" /Volumes/web/cnidarian/{R2}_fastqc/fastqc_data.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">>Overrepresented sequences\twarn\r\n", "#Sequence\tCount\tPercentage\tPossible Source\r\n", "GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\t21905\t0.6351447741546384\tIllumina Single End PCR Primer 1 (100% over 36bp)\r\n", "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t9464\t0.27441269767630666\tNo Hit\r\n", "GATCGGAAGAGCGTCGGGTAGGGAAAGAGGGTAGAT\t7464\t0.2164218486322858\tIllumina Single End PCR Primer 1 (96% over 29bp)\r\n", "GATCGGAAGAGCGTCGGGTAGGGAAAGAGTGTAGAT\t6997\t0.20288098538050695\tIllumina Single End PCR Primer 1 (97% over 36bp)\r\n", ">>END_MODULE\r\n" ] } ], "prompt_number": 18 }, { "cell_type": "code", "collapsed": false, "input": [ "!sed -n \"/>>Overrepresented/,/>>END_MODULE/p\" /Volumes/web/cnidarian/{R2}_fastqc/fastqc_data.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">>Overrepresented sequences\twarn\r\n", "#Sequence\tCount\tPercentage\tPossible Source\r\n", "GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\t21905\t0.6351447741546384\tIllumina Single End PCR Primer 1 (100% over 36bp)\r\n", "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\t9464\t0.27441269767630666\tNo Hit\r\n", "GATCGGAAGAGCGTCGGGTAGGGAAAGAGGGTAGAT\t7464\t0.2164218486322858\tIllumina Single End PCR Primer 1 (96% over 29bp)\r\n", "GATCGGAAGAGCGTCGGGTAGGGAAAGAGTGTAGAT\t6997\t0.20288098538050695\tIllumina Single End PCR Primer 1 (97% over 36bp)\r\n", ">>END_MODULE\r\n" ] } ], "prompt_number": 8 }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Removing Overpresented sequences" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!cat /Volumes/web/cnidarian/YE_overrepresent.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">TruSeq Adapter, Index 1\r\n", "GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTG\r\n", ">Illumina Single End PCR Primer 1\r\n", "GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGAT\r\n" ] } ], "prompt_number": 10 }, { "cell_type": "code", "collapsed": false, "input": [ "!/Volumes/Bay3/Software/ea-utils.1.1.2-537/fastq-mcf \\\n", "-o /Volumes/web/cnidarian/{R1}_tr.fastq \\\n", "-o /Volumes/web/cnidarian/{R2}_tr.fastq \\\n", "/Volumes/web/cnidarian/YE_overrepresent.txt \\\n", "/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/{R1}.fastq \\\n", "/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/{R2}.fastq" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Scale used: 2.2\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Phred: 33\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Within-read Skew: Position 4 from the start of reads is skewed!\r\n", "Within-read Skew: Position 5 from the start of reads is skewed!\r\n", "Within-read Skew: Position 6 from the start of reads is skewed!\r\n", "Within-read Skew: Position 7 from the start of reads is skewed!\r\n", "Within-read Skew: Position 8 from the start of reads is skewed!\r\n", "Within-read Skew: Position 9 from the start of reads is skewed!\r\n", "Within-read Skew: Position 10 from the start of reads is skewed!\r\n", "Within-read Skew: Position 12 from the start of reads is skewed!\r\n", "Within-read Skew: Position 14 from the start of reads is skewed!\r\n", "Within-read Skew: Position 16 from the start of reads is skewed!\r\n", "Within-read Skew: Position 17 from the start of reads is skewed!\r\n", "Within-read Skew: Position 4 from the end of reads is skewed!\r\n", "Within-read Skew: Position 6 from the end of reads is skewed!\r\n", "Within-read Skew: Position 7 from the end of reads is skewed!\r\n", "Within-read Skew: Position 8 from the end of reads is skewed!\r\n", "Within-read Skew: Position 11 from the end of reads is skewed!\r\n", "Within-read Skew: Position 13 from the end of reads is skewed!\r\n", "Within-read Skew: Position 14 from the end of reads is skewed!\r\n", "Within-read Skew: Position 15 from the end of reads is skewed!\r\n", "Within-read Skew: Position 16 from the end of reads is skewed!\r\n", "Warning: Too much skewing found (36), disabling skew clipping\r\n", "Threshold used: 751 out of 300000\r\n", "Adapter TruSeq Adapter, Index 1 (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTG): counted 8753 at the 'start' of '/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y38_control_GTGAAA_L005_R1.fastq', clip set to 4\r\n", "Files: 2\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Total reads: 3448820\r\n", "Too short after clip: 186681\r\n", "Clipped 'start' reads (/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y38_control_GTGAAA_L005_R1.fastq): Count 993, Mean: 4.51, Sd: 1.78\r\n", "Trimmed 68594 reads (/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y38_control_GTGAAA_L005_R1.fastq) by an average of 7.77 bases on quality < 7\r\n", "Trimmed 140063 reads (/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/filtered_Y38_control_GTGAAA_L005_R2.fastq) by an average of 21.59 bases on quality < 7\r\n" ] } ], "prompt_number": 19 }, { "cell_type": "code", "collapsed": false, "input": [ "#confirming\n", "!/Volumes/Bay3/Software/FastQC/fastqc \\\n", "/Volumes/web/cnidarian/{R1}_tr.fastq \\\n", "-q \\\n", "-o /Volumes/web/cnidarian/" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 25 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep -A 5 \"Overrepresented\" /Volumes/web/cnidarian/{R1}_tr_fastqc/fastqc_data.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">>Overrepresented sequences\tpass\r\n", ">>END_MODULE\r\n", ">>Kmer Content\tfail\r\n", "#Sequence\tCount\tObs/Exp Overall\tObs/Exp Max\tMax Obs/Exp Position\r\n", "CCCCC\t50\t509094.34\t1651751.6\t32\r\n", "CTCCC\t130\t10524.399\t324060.84\t24\r\n" ] } ], "prompt_number": 26 }, { "cell_type": "code", "collapsed": false, "input": [ "#confirming\n", "!/Volumes/Bay3/Software/FastQC/fastqc \\\n", "/Volumes/web/cnidarian/{R2}_tr.fastq \\\n", "-q \\\n", "-o /Volumes/web/cnidarian/" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 27 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep -A 5 \"Overrepresented\" /Volumes/web/cnidarian/{R2}_tr_fastqc/fastqc_data.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">>Overrepresented sequences\tpass\r\n", ">>END_MODULE\r\n", ">>Kmer Content\tfail\r\n", "#Sequence\tCount\tObs/Exp Overall\tObs/Exp Max\tMax Obs/Exp Position\r\n", "GGGGG\t60\t331473.72\t4440570.5\t27\r\n", "GAGGG\t235\t11672.065\t199613.89\t27\r\n" ] } ], "prompt_number": 28 }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "BSMAP" ] }, { "cell_type": "code", "collapsed": false, "input": [ "! /Volumes/Bay3/Software/BSMAP/bsmap-2.74/bsmap \\\n", "-a /Volumes/web/cnidarian/{R1}_tr.fastq \\\n", "-b /Volumes/web/cnidarian/{R2}_tr.fastq \\\n", "-d /Volumes/web/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa.gz \\\n", "-o /Volumes/web/cnidarian/BiLar_YE_control_t.sam \\\n", "-p 4" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\r\n", "BSMAP v2.74\r\n", "Start at: Tue Jun 3 15:33:16 2014\r\n", "\r\n", "Input reference file: /Volumes/web/cnidarian/oyster.v9.fa" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " \t(format: FASTA)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Load in 11969 db seqs, total size 558601156 bp. 30 secs passed\r\n", "total_kmers: 43046721\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Create seed table. 119 secs passed\r\n", "max number of mismatches: read_length * 8% \tmax gap size: 0\r\n", "kmer cut-off ratio: 5e-07\r\n", "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\r\n", "quality cutoff: 0\tbase quality char: '!'\r\n", "min fragment size:28\tmax fragemt size:500\r\n", "start from read #1\tend at read #4294967295\r\n", "additional alignment: T in reads => C in reference\r\n", "mapping strand (read_1): ++,-+\r\n", "mapping strand (read_2): +-,--\r\n", "Pair-end alignment(4 threads)\r\n", "Input read file #1: /Volumes/web/cnidarian/filtered_Y54_Mix_GTGGCC_L005_R1_tr.fastq \t(format: FASTQ)\r\n", "Input read file #2: /Volumes/web/cnidarian/filtered_Y54_Mix_GTGGCC_L005_R2_tr.fastq" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " \t(format: FASTQ)\r\n", "Output file: /Volumes/web/cnidarian/BiLar_YE_mix_t.sam\t (format: SAM)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t50000 read pairs finished. 290 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t150000 read pairs finished. 294 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t100000 read pairs finished. 294 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t200000 read pairs finished. 297 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"output_type": "stream", "stream": "stdout", "text": [ "3: \t12650000 read pairs finished. 8688 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t12700000 read pairs finished. 8744 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t12750000 read pairs finished. 8750 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t12800000 read pairs finished. 8799 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t12850000 read pairs finished. 8813 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t12900000 read pairs finished. 8868 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t12950000 read pairs finished. 8875 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t13000000 read pairs finished. 8924 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t13050000 read pairs finished. 8938 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t13100000 read pairs finished. 8994 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t13150000 read pairs finished. 9002 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t13200000 read pairs finished. 9050 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t13250000 read pairs finished. 9067 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t13412322 read pairs finished. 9098 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t13300000 read pairs finished. 9115 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t13350000 read pairs finished. 9121 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t13400000 read pairs finished. 9136 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Total number of aligned reads: \r\n", "pairs: 7934451 (59%)\r\n", "single a: 2762270 (21%)\r\n", "single b: 2440630 (18%)\r\n", "Done.\r\n", "Finished at Tue Jun 3 18:05:32 2014\r\n", "Total time consumed: 9136 secs\r\n" ] } ], "prompt_number": 55 }, { "cell_type": "code", "collapsed": false, "input": [ "! /Users/Shared/Apps/bsmap-2.74/bsmap \\\n", "-a /Volumes/web/cnidarian/{R1}_tr.fastq \\\n", "-b /Volumes/web/cnidarian/{R2}_tr.fastq \\\n", "-d /Volumes/web/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa.gz \\\n", "-o /Volumes/web/cnidarian/BiLar_YE_control_t.sam \\\n", "-p 8" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "\r\n", "BSMAP v2.74\r\n", "Start at: Fri Jun 6 08:18:53 2014\r\n", "\r\n", "Input reference file: /Volumes/web/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa.gz \t(format: gzipped FASTA)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Load in 7658 db seqs, total size 557717710 bp. 15 secs passed\r\n", "total_kmers: 43046721\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Create seed table. 33 secs passed\r\n", "max number of mismatches: read_length * 8% \tmax gap size: 0\r\n", "kmer cut-off ratio: 5e-07\r\n", "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\r\n", "quality cutoff: 0\tbase quality char: '!'\r\n", "min fragment size:28\tmax fragemt size:500\r\n", "start from read #1\tend at read #4294967295\r\n", "additional alignment: T in reads => C in reference\r\n", "mapping strand (read_1): ++,-+\r\n", "mapping strand (read_2): +-,--\r\n", "Pair-end alignment(8 threads)\r\n", "Input read file #1: /Volumes/web/cnidarian/filtered_Y38_control_GTGAAA_L005_R1_tr.fastq" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " \t(format: FASTQ)\r\n", "Input read file #2: /Volumes/web/cnidarian/filtered_Y38_control_GTGAAA_L005_R2_tr.fastq \t(format: FASTQ)\r\n", "Output file: /Volumes/web/cnidarian/BiLar_YE_control_t.sam\t (format: SAM)\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t50000 read pairs finished. 80 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t100000 read pairs finished. 83 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t150000 read pairs finished. 84 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #4: \t200000 read pairs finished. 85 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #5: \t250000 read pairs finished. 87 secs passed\r\n" ] }, { "output_type": 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"stream": "stdout", "text": [ "Thread #5: \t2650000 read pairs finished. 403 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #7: \t2700000 read pairs finished. 407 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #6: \t2750000 read pairs finished. 417 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t2800000 read pairs finished. 422 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t2850000 read pairs finished. 451 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t2900000 read pairs finished. 453 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #3: \t2950000 read pairs finished. 457 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #4: \t3000000 read pairs finished. 458 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #5: \t3050000 read pairs finished. 459 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #7: \t3100000 read pairs finished. 461 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #0: \t3262139 read pairs finished. 462 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #6: \t3150000 read pairs finished. 464 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #2: \t3200000 read pairs finished. 465 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Thread #1: \t3250000 read pairs finished. 471 secs passed\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Total number of aligned reads: \r\n", "pairs: 1817795 (56%)\r\n", "single a: 771957 (24%)\r\n", "single b: 635567 (19%)\r\n", "Done.\r\n", "Finished at Fri Jun 6 08:26:44 2014\r\n", "Total time consumed: 471 secs\r\n" ] } ], "prompt_number": 3 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/BiLar_YE_control_t.sam" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "@HD\tVN:1.0\r\n", "@SQ\tSN:C12728\tLN:200\r\n", "@SQ\tSN:C12722\tLN:200\r\n", "@SQ\tSN:C12706\tLN:200\r\n", "@SQ\tSN:C12718\tLN:200\r\n", "@SQ\tSN:C12732\tLN:200\r\n", "@SQ\tSN:C12726\tLN:200\r\n", "@SQ\tSN:C12708\tLN:200\r\n", "@SQ\tSN:C12730\tLN:200\r\n", "@SQ\tSN:C12724\tLN:200\r\n" ] } ], "prompt_number": 2 }, { "cell_type": "code", "collapsed": false, "input": [ "#where is bsmap\n", "#bsmap=\"/Users/Shared/Apps/bsmap-2.74/\"\n", "bsmap=\"/Volumes/Bay3/Software/BSMAP/bsmap-2.74/\"\n", "\n", "#genome\n", "#genome=\"/Users/Steven/Downloads/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa\"\n", "genome=\"/Volumes/web/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 3 }, { "cell_type": "code", "collapsed": false, "input": [ "!python {bsmap}methratio.py -d {genome} -u -z -g -o /Volumes/web/cnidarian/YE_control_22sm_methratio_out.txt -s {bsmap}samtools /Volumes/web/cnidarian/BiLar_YE_control_t.sam\n" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "@ Fri Jun 6 08:34:48 2014: reading reference /Volumes/web/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Fri Jun 6 08:36:31 2014: reading /Volumes/web/cnidarian/BiLar_YE_control_t.sam ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "[samopen] SAM header is present: 7658 sequences.\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Fri Jun 6 08:44:24 2014: combining CpG methylation from both strands ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Fri Jun 6 08:45:40 2014: writing /Volumes/web/cnidarian/YE_control_22sm_methratio_out.txt ...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "@ Fri Jun 6 08:52:48 2014: done.\r\n", "total 3509466 valid mappings, 16975201 covered cytosines, average coverage: 1.15 fold.\r\n" ] } ], "prompt_number": 4 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/YE_control_22sm_methratio_out.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "chr\tpos\tstrand\tcontext\tratio\teff_CT_count\tC_count\tCT_count\trev_G_count\trev_GA_count\tCI_lower\tCI_upper\r\n", "C12798\t41\t+\tAACAA\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12798\t45\t+\tAACTT\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12798\t52\t+\tATCCC\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12798\t53\t+\tTCCCC\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12798\t54\t+\tCCCCT\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12798\t55\t+\tCCCTT\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12798\t58\t+\tTTCAC\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12798\t60\t+\tCACCT\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12798\t61\t+\tACCTA\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n" ] } ], "prompt_number": 5 }, { "cell_type": "code", "collapsed": false, "input": [ "#command for only obtaining the context '__CG_'\n", "#!grep \"[A-Z][A-Z]CG[A-Z]\" /Volumes/web/cnidarian/YE_mix_22sm_methratio_outCG.txt \n", "#5x coverage\n", "!awk '{if ($8 >= 3) print $1,$2-1,$2+1,\"CpG\",$5}' /Volumes/web/cnidarian/YE_control_22sm_outCG3x.igv \n", "!tr ' ' \"\\t\" /Volumes/web/cnidarian/filt_YE_control_22smCG3x.igv" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 61 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/YE_mix_22sm_methratio_out.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "chr\tpos\tstrand\tcontext\tratio\teff_CT_count\tC_count\tCT_count\trev_G_count\trev_GA_count\tCI_lower\tCI_upper\r\n", "C12706\t112\t+\tTTCTA\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12706\t135\t+\tGACTC\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12706\t137\t+\tCTCTT\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12706\t148\t+\tATCAA\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12706\t151\t+\tAACTT\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12706\t159\t+\tAGCCT\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12706\t160\t+\tGCCTA\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12706\t163\t+\tTACAA\t0.000\t1.00\t0\t1\t0\t0\t0.000\t0.793\r\n", "C12706\t170\t-\tAAGGT\t0.000\t1.00\t0\t1\t2\t2\t0.000\t0.793\r\n" ] } ], "prompt_number": 5 }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "#command for only obtaining the context '__CG_'\n", "#!grep \"[A-Z][A-Z]CG[A-Z]\" /Volumes/web/cnidarian/YE_mix_22sm_methratio_outCG.txt \n", "#5x coverage\n", "!awk '{if ($8 >= 3) print $1\"_\"$2-1,$1,$2-1,$2+1,\"CpG\",$5}' /Volumes/web/cnidarian/YE_mix_22sm_outCG3x.igv \n", "!tr ' ' \"\\t\" /Volumes/web/cnidarian/filt_YE_mix_22smCG3xj.txt" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 26 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/filt_YE_mix_22smCG3xj.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C12764_118\tC12764\t118\t120\tCpG\t0.000\r\n", "C12764_128\tC12764\t128\t130\tCpG\t0.000\r\n", "C12764_131\tC12764\t131\t133\tCpG\t0.000\r\n", "C12778_113\tC12778\t113\t115\tCpG\t0.000\r\n", "C12802_118\tC12802\t118\t120\tCpG\t0.000\r\n", "C12860_104\tC12860\t104\t106\tCpG\t0.000\r\n", "C12860_112\tC12860\t112\t114\tCpG\t0.000\r\n", "C12860_115\tC12860\t115\t117\tCpG\t0.000\r\n", "C12860_120\tC12860\t120\t122\tCpG\t0.000\r\n", "C12860_158\tC12860\t158\t160\tCpG\t0.000\r\n" ] } ], "prompt_number": 27 }, { "cell_type": "code", "collapsed": false, "input": [ "#command for only obtaining the context '__CG_'\n", "#!grep \"[A-Z][A-Z]CG[A-Z]\" /Volumes/web/cnidarian/YE_control_22sm_methratio_outCG.txt \n", "#5x coverage\n", "!awk '{if ($8 >= 3) print $1\"_\"$2-1,$1,$2-1,$2+1,\"CpG\",$5}' /Volumes/web/cnidarian/YE_control_22sm_outCG3x.igv \n", "!tr ' ' \"\\t\" /Volumes/web/cnidarian/filt_YE_control_22smCG3xj.txt" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 28 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/filt_YE_control_22smCG3xj.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C13288_100\tC13288\t100\t102\tCpG\t0.000\r\n", "C13288_107\tC13288\t107\t109\tCpG\t0.000\r\n", "C13448_36\tC13448\t36\t38\tCpG\t0.000\r\n", "C13800_97\tC13800\t97\t99\tCpG\t0.000\r\n", "C14308_113\tC14308\t113\t115\tCpG\t0.000\r\n", "C14308_120\tC14308\t120\t122\tCpG\t0.000\r\n", "C14966_93\tC14966\t93\t95\tCpG\t0.000\r\n", "C15066_81\tC15066\t81\t83\tCpG\t0.333\r\n", "C15066_88\tC15066\t88\t90\tCpG\t0.000\r\n", "C15066_260\tC15066\t260\t262\tCpG\t0.000\r\n" ] } ], "prompt_number": 30 }, { "cell_type": "code", "collapsed": false, "input": [ "spd=\"/Users/sr320/sqlshare-pythonclient/tools/\" " ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 12 }, { "cell_type": "code", "collapsed": false, "input": [ "!python {spd}singleupload.py -d filt_YE_control_22smCG3x /Volumes/web/cnidarian/filt_YE_control_22smCG3xj.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "processing chunk line 0 to 77742 (0.0385191440582 s elapsed)\r\n", "pushing /Volumes/web/cnidarian/filt_YE_control_22smCG3xj.txt...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "parsing 41B4A049...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "finished filt_YE_control_22smCG3x\r\n" ] } ], "prompt_number": 31 }, { "cell_type": "code", "collapsed": false, "input": [ "!python {spd}singleupload.py -d filt_YE_mix_22smCG3x /Volumes/web/cnidarian/filt_YE_mix_22smCG3xj.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "processing chunk line 0 to 1434021 (8.93834710121 s elapsed)\r\n", "pushing /Volumes/web/cnidarian/filt_YE_mix_22smCG3xj.txt...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "parsing ED260C3F...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "finished filt_YE_mix_22smCG3x\r\n" ] } ], "prompt_number": 32 }, { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "SQLShare Join\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "`\n", "SELECT * FROM [sr320@washington.edu].[filt_YE_control_22smCG3x]c\n", " left join\n", " [sr320@washington.edu].[filt_YE_mix_22smCG3x]m\n", " on\n", " c.Column1=m.Column1\n", " where m.Column1 <> ' '\n", "` " ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/YE_mvc_3xjoin.csv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Column1,Column2,Column3,Column4,Column5,Column6,Column1,Column2,Column3,Column4,Column5,Column6\r", "\r\n", "C14308_113,C14308,113,115,CpG,0.000,C14308_113,C14308,113,115,CpG,0.000\r", "\r\n", "C15156_18,C15156,18,20,CpG,0.000,C15156_18,C15156,18,20,CpG,0.000\r", "\r\n", "C15156_23,C15156,23,25,CpG,0.000,C15156_23,C15156,23,25,CpG,0.000\r", "\r\n", "C15646_218,C15646,218,220,CpG,0.000,C15646_218,C15646,218,220,CpG,0.000\r", "\r\n", "C15646_223,C15646,223,225,CpG,0.250,C15646_223,C15646,223,225,CpG,0.000\r", "\r\n", "C15646_282,C15646,282,284,CpG,0.000,C15646_282,C15646,282,284,CpG,0.000\r", "\r\n", "C15646_284,C15646,284,286,CpG,0.000,C15646_284,C15646,284,286,CpG,0.000\r", "\r\n", "C15646_293,C15646,293,295,CpG,0.000,C15646_293,C15646,293,295,CpG,0.000\r", "\r\n", "C15646_295,C15646,295,297,CpG,0.000,C15646_295,C15646,295,297,CpG,0.000\r", "\r\n" ] } ], "prompt_number": 33 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc -l /Volumes/web/cnidarian/YE_mvc_3xjoin.csv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 35430 /Volumes/web/cnidarian/YE_mvc_3xjoin.csv\r\n" ] } ], "prompt_number": 34 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/YE_mixHYPO.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "ratio_control\tColumn1\tColumn2\tColumn3\tColumn4\tColumn5\tratio_mix\r\n", "1\tC26536_1511\tC26536\t1511\t1513\tCpG\t0\r\n", "1\tscaffold1179_1120799\tscaffold1179\t1120799\t1120801\tCpG\t0\r\n", "1\tscaffold1189_665949\tscaffold1189\t665949\t665951\tCpG\t0\r\n", "1\tscaffold1532_1178565\tscaffold1532\t1178565\t1178567\tCpG\t0\r\n", "1\tscaffold1532_888871\tscaffold1532\t888871\t888873\tCpG\t0\r\n", "1\tscaffold1656_129879\tscaffold1656\t129879\t129881\tCpG\t0\r\n", "1\tscaffold1682_233873\tscaffold1682\t233873\t233875\tCpG\t0\r\n", "1\tscaffold1733_67696\tscaffold1733\t67696\t67698\tCpG\t0\r\n", "1\tscaffold1860_178219\tscaffold1860\t178219\t178221\tCpG\t0\r\n" ] } ], "prompt_number": 35 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc -l /Volumes/web/cnidarian/YE_mixHYPO.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 279 /Volumes/web/cnidarian/YE_mixHYPO.txt\r\n" ] } ], "prompt_number": 38 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/YE_mixHYPER.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "ratio_control\tColumn1\tColumn2\tColumn3\tColumn4\tColumn5\tratio_mix\r\n", "0\tC27742_4663\tC27742\t4663\t4665\tCpG\t1\r\n", "0\tscaffold1021_12097\tscaffold1021\t12097\t12099\tCpG\t1\r\n", "0\tscaffold1032_211526\tscaffold1032\t211526\t211528\tCpG\t1\r\n", "0\tscaffold105_434416\tscaffold105\t434416\t434418\tCpG\t1\r\n", "0\tscaffold1086_656185\tscaffold1086\t656185\t656187\tCpG\t1\r\n", "0\tscaffold1086_656188\tscaffold1086\t656188\t656190\tCpG\t1\r\n", "0\tscaffold1087_9508\tscaffold1087\t9508\t9510\tCpG\t1\r\n", "0\tscaffold109_358907\tscaffold109\t358907\t358909\tCpG\t1\r\n", "0\tscaffold1132_613494\tscaffold1132\t613494\t613496\tCpG\t1\r\n" ] } ], "prompt_number": 36 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc -l /Volumes/web/cnidarian/YE_mixHYPER.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 544 /Volumes/web/cnidarian/YE_mixHYPER.txt\r\n" ] } ], "prompt_number": 39 }, { "cell_type": "code", "collapsed": false, "input": [ "#make a mix_hyper igv track.." ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 40 }, { "cell_type": "code", "collapsed": false, "input": [ "!awk '{print $3,$4,$5,$6,$7}' /Volumes/web/cnidarian/YE_mixHYPER.igv \n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 43 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/YE_mixHYPER.igv " ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Column2 Column3 Column4 Column5 ratio_mix\r\n", "C27742 4663 4665 CpG 1\r\n", "scaffold1021 12097 12099 CpG 1\r\n", "scaffold1032 211526 211528 CpG 1\r\n", "scaffold105 434416 434418 CpG 1\r\n", "scaffold1086 656185 656187 CpG 1\r\n", "scaffold1086 656188 656190 CpG 1\r\n", "scaffold1087 9508 9510 CpG 1\r\n", "scaffold109 358907 358909 CpG 1\r\n", "scaffold1132 613494 613496 CpG 1\r\n" ] } ], "prompt_number": 44 }, { "cell_type": "code", "collapsed": false, "input": [ "!tail -n +2 /Volumes/web/cnidarian/YE_mixHYPER.igv > /Volumes/web/cnidarian/YE_mixHYPERc.igv " ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 46 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/YE_mixHYPERc.igv " ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C27742 4663 4665 CpG 1\r\n", "scaffold1021 12097 12099 CpG 1\r\n", "scaffold1032 211526 211528 CpG 1\r\n", "scaffold105 434416 434418 CpG 1\r\n", "scaffold1086 656185 656187 CpG 1\r\n", "scaffold1086 656188 656190 CpG 1\r\n", "scaffold1087 9508 9510 CpG 1\r\n", "scaffold109 358907 358909 CpG 1\r\n", "scaffold1132 613494 613496 CpG 1\r\n", "scaffold1142 97241 97243 CpG 1\r\n" ] } ], "prompt_number": 47 }, { "cell_type": "code", "collapsed": false, "input": [ "!awk '{print $1,$2,$3,\"HYPER\"}' /Volumes/web/cnidarian/YE_mixHYPER.bed \n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 58 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/YE_mixHYPER.bed " ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C27742 4663 4665 HYPER\r\n", "scaffold1021 12097 12099 HYPER\r\n", "scaffold1032 211526 211528 HYPER\r\n", "scaffold105 434416 434418 HYPER\r\n", "scaffold1086 656185 656187 HYPER\r\n", "scaffold1086 656188 656190 HYPER\r\n", "scaffold1087 9508 9510 HYPER\r\n", "scaffold109 358907 358909 HYPER\r\n", "scaffold1132 613494 613496 HYPER\r\n", "scaffold1142 97241 97243 HYPER\r\n" ] } ], "prompt_number": 59 }, { "cell_type": "code", "collapsed": false, "input": [ "#make a mix_hypo igv track.." ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "!awk '{print $3,$4,$5,$6,-$1}' /Volumes/web/cnidarian/YE_mixHYPO.igv \n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 48 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/YE_mixHYPO.igv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Column2 Column3 Column4 Column5 -0\r\n", "C26536 1511 1513 CpG -1\r\n", "scaffold1179 1120799 1120801 CpG -1\r\n", "scaffold1189 665949 665951 CpG -1\r\n", "scaffold1532 1178565 1178567 CpG -1\r\n", "scaffold1532 888871 888873 CpG -1\r\n", "scaffold1656 129879 129881 CpG -1\r\n", "scaffold1682 233873 233875 CpG -1\r\n", "scaffold1733 67696 67698 CpG -1\r\n", "scaffold1860 178219 178221 CpG -1\r\n" ] } ], "prompt_number": 51 }, { "cell_type": "code", "collapsed": false, "input": [ "!tail -n +2 /Volumes/web/cnidarian/YE_mixHYPO.igv > /Volumes/web/cnidarian/YE_mixHYPOc.igv" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 52 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/YE_mixHYPOc.igv" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "C26536 1511 1513 CpG -1\r\n", "scaffold1179 1120799 1120801 CpG -1\r\n", "scaffold1189 665949 665951 CpG -1\r\n", "scaffold1532 1178565 1178567 CpG -1\r\n", "scaffold1532 888871 888873 CpG -1\r\n", "scaffold1656 129879 129881 CpG -1\r\n", "scaffold1682 233873 233875 CpG -1\r\n", "scaffold1733 67696 67698 CpG -1\r\n", "scaffold1860 178219 178221 CpG -1\r\n", "scaffold1891 93285 93287 CpG -1\r\n" ] } ], "prompt_number": 53 }, { "cell_type": "code", "collapsed": false, "input": [ "!awk '{print $1,$2,$3,\"HYPO\"}' /Volumes/web/cnidarian/YE_mixHYPO.bed \n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 60 }, { "cell_type": "code", "collapsed": false, "input": [ "!intersectbed" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/bin/sh: intersectbed: command not found\r\n" ] } ], "prompt_number": 55 }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }