{ "metadata": { "name": "", "signature": "sha256:f059df9c829fd6580f94ed465d3d5e1b10032016fbbf9316daae743ed8dd474a" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "Replicating BiGO_larvae concatenation" ] }, { "cell_type": "code", "collapsed": false, "input": [ "M1_R1" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "#Claire's M1_R1\n", "!head /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "@HWI-ST700693:373:C39EMACXX:4:1101:15213:2222\r\n", "TTTTAATAAGAATTATTGATAAAGAAGTATTTGTATATGTTTGAATTGGTTTATTTTGTTTTTTTTTGAAATGATA\r\n", "+\r\n", "4:BD42243323ACCDDD?CDDDEEDDC\r\n", "@HWI-ST700693:351:D2CA8ACXX:7:1101:2200:2105\r\n", "TTTAATATAAATTATATATAAAATTGTTTGAGGTAAAGAAAAAATATTAGTTAATATTTAATATATTGTGTTAGTT\r\n", "+\r\n", "BBCFDFFFHHHHHJJJJJJJJJJJJJJJJHEHIAFGCHIIJIJJJJJJJJIJJJIIJJJJJJIJJJJJGIIHJJGB\r\n", "@HWI-ST700693:351:D2CA8ACXX:7:1101:2596:2201\r\n", "GATTTTTTATTTTTAATTTAATTAATATGGTTATTTAAAAATGGGTTGAATTTGTTTGATGAGAGGGGAGATAGGT\r\n" ] } ], "prompt_number": 11 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R1a.fastq" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 33188808 33188808 1680104182 /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R1a.fastq\r\n" ] } ], "prompt_number": 12 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep -c \"@HWI\" /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R1a.fastq" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "8297202\r\n" ] } ], "prompt_number": 14 }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "T3D5" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq " ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 29402580 29402580 1488447849 /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq\r\n" ] } ], "prompt_number": 15 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_R1a.fastq" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 29402580 29402580 1488447849 /Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_R1a.fastq\r\n" ] } ], "prompt_number": 16 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep -c \"@HWI\" /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq " ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "7350645\r\n" ] } ], "prompt_number": 17 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep -c \"@HWI\" /Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_R1a.fastq" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "7350645\r\n" ] } ], "prompt_number": 18 }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Removing Adaptors from concatenated files" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!/Users/sr320/galaxy-dist/tools/fastq/fastq_trimmer.py" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "/bin/sh: /Users/sr320/galaxy-dist/tools/fastq/fastq_trimmer.py: Permission denied\r\n" ] } ], "prompt_number": 1 }, { "cell_type": "code", "collapsed": false, "input": [ "!/Volumes/Bay3/Software/bin/fastx_clipper -h" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "usage: fastx_clipper [-h] [-a ADAPTER] [-D] [-l N] [-n] [-d N] [-c] [-C] [-o] [-v] [-z] [-i INFILE] [-o OUTFILE]\r\n", "Part of FASTX Toolkit 0.0.13 by A. Gordon (gordon@cshl.edu)\r\n", "\r\n", " [-h] = This helpful help screen.\r\n", " [-a ADAPTER] = ADAPTER string. default is CCTTAAGG (dummy adapter).\r\n", " [-l N] = discard sequences shorter than N nucleotides. default is 5.\r\n", " [-d N] = Keep the adapter and N bases after it.\r\n", " (using '-d 0' is the same as not using '-d' at all. which is the default).\r\n", " [-c] = Discard non-clipped sequences (i.e. - keep only sequences which contained the adapter).\r\n", " [-C] = Discard clipped sequences (i.e. - keep only sequences which did not contained the adapter).\r\n", " [-k] = Report Adapter-Only sequences.\r\n", " [-n] = keep sequences with unknown (N) nucleotides. default is to discard such sequences.\r\n", " [-v] = Verbose - report number of sequences.\r\n", " If [-o] is specified, report will be printed to STDOUT.\r\n", " If [-o] is not specified (and output goes to STDOUT),\r\n", " report will be printed to STDERR.\r\n", " [-z] = Compress output with GZIP.\r\n", " [-D]\t = DEBUG output.\r\n", " [-M N] = require minimum adapter alignment length of N.\r\n", " If less than N nucleotides aligned with the adapter - don't clip it. [-i INFILE] = FASTA/Q input file. default is STDIN.\r\n", " [-o OUTFILE] = FASTA/Q output file. default is STDOUT.\r\n", "\r\n" ] } ], "prompt_number": 3 }, { "cell_type": "code", "collapsed": false, "input": [ "!/Volumes/Bay3/Software/ea-utils.1.1.2-537/fastq-clipper" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "usage: fastq-clipper [options] \r\n", "\r\n", "Removes one or more adapter sequences from the fastq file.\r\n", "Adapter sequences are colon-delimited.\r\n", "Stats go to stderr, unless -o is specified.\r\n", "\r\n", "Options:\r\n", "\t-h\tThis help\r\n", "\t-o FIL\tOutput file (stats to stdout)\r\n", "\t-p N\tMaximum difference percentage (10)\r\n", "\t-m N\tMinimum clip length (1)\r\n", "\t-l N\tMinimum remaining sequence length (15)\r\n", "\t-x [N]\tExtra match length past adapter length, \r\n", "\t\t N =-1 : search all\r\n", "\t\t N = 0 : search only up to adapter length\r\n", "\t-e\tEnd-of-line (default)\r\n", "\t-b\tBeginning-of-line (not supported yet)\r\n" ] } ], "prompt_number": 4 }, { "cell_type": "code", "collapsed": false, "input": [ "!/Volumes/Bay3/Software/ea-utils.1.1.2-537/fastq-mcf -o /Volumes/web/cnidarian/test_adp /Volumes/web/Mollusk/bs_larvae_exp/Adapters_LarvaeSequencingFiles.txt /Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_R1a.fastq\n" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Comparing pre and post" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_R1a.fastq" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 29402580 29402580 1488447849 /Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_R1a.fastq\r\n" ] } ], "prompt_number": 9 }, { "cell_type": "code", "collapsed": false, "input": [ "!wc /Volumes/web/cnidarian/test_adp" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 28807196 28807196 1439780747 /Volumes/web/cnidarian/test_adp\r\n" ] } ], "prompt_number": 10 }, { "cell_type": "markdown", "metadata": {}, "source": [ "post\n", "\"FastQC_18EC6333.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "pre \"FastQC_18EC6493.png\"/" ] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Trimming all files" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!ls /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "F_R1.fastq M3_R1.fastq T1D5_R1.fastq T3D5_R1.fastq\r\n", "M1_R1.fastq T1D3_R1.fastq T3D3_R1.fastq\r\n" ] } ], "prompt_number": 11 }, { "cell_type": "code", "collapsed": false, "input": [ "!ls /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "F_R2.fastq M3_R2.fastq T1D5_R2.fastq T3D5_R2.fastq\r\n", "M1_R2.fastq T1D3_R2.fastq T3D3_R2.fastq\r\n" ] } ], "prompt_number": 12 }, { "cell_type": "code", "collapsed": false, "input": [ "#variables\n", "lib=\"M1\"\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 13 }, { "cell_type": "code", "collapsed": false, "input": [ "!/Volumes/Bay3/Software/ea-utils.1.1.2-537/fastq-mcf \\\n", "-o /Volumes/web/cnidarian/mcf_{lib}_R1.fastq \\\n", "-o /Volumes/web/cnidarian/mcf_{lib}_R2.fastq \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Adapters_LarvaeSequencingFiles.txt \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/{lib}_R1.fastq \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/{lib}_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 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 18 from the start of reads is skewed!\r\n", "Within-read Skew: Position 19 from the start of reads is skewed!\r\n", "Within-read Skew: Position 20 from the start of reads is skewed!\r\n", "Within-read Skew: Position 21 from the start of reads is skewed!\r\n", "Within-read Skew: Position 22 from the start of reads is skewed!\r\n", "Within-read Skew: Position 23 from the start of reads is skewed!\r\n", "Within-read Skew: Position 24 from the start of reads is skewed!\r\n", "Within-read Skew: Position 25 from the start of reads is skewed!\r\n", "Within-read Skew: Position 26 from the start of reads is skewed!\r\n", "Within-read Skew: Position 27 from the start of reads is skewed!\r\n", "Within-read Skew: Position 28 from the start of reads is skewed!\r\n", "Within-read Skew: Position 29 from the start of reads is skewed!\r\n", "Within-read Skew: Position 30 from the start of reads is skewed!\r\n", "Within-read Skew: Position 31 from the start of reads is skewed!\r\n", "Within-read Skew: Position 32 from the start of reads is skewed!\r\n", "Within-read Skew: Position 33 from the start of reads is skewed!\r\n", "Within-read Skew: Position 34 from the start of reads is skewed!\r\n", "Within-read Skew: Position 35 from the start of reads is skewed!\r\n", "Within-read Skew: Position 36 from the start of reads is skewed!\r\n", "Within-read Skew: Position 37 from the start of reads is skewed!\r\n", "Within-read Skew: Position 17 from the end of reads is skewed!\r\n", "Within-read Skew: Position 18 from the end of reads is skewed!\r\n", "Within-read Skew: Position 20 from the end of reads is skewed!\r\n", "Within-read Skew: Position 21 from the end of reads is skewed!\r\n", "Within-read Skew: Position 23 from the end of reads is skewed!\r\n", "Within-read Skew: Position 24 from the end of reads is skewed!\r\n", "Within-read Skew: Position 27 from the end of reads is skewed!\r\n", "Within-read Skew: Position 28 from the end of reads is skewed!\r\n", "Within-read Skew: Position 29 from the end of reads is skewed!\r\n", "Within-read Skew: Position 30 from the end of reads is skewed!\r\n", "Within-read Skew: Position 31 from the end of reads is skewed!\r\n", "Within-read Skew: Position 32 from the end of reads is skewed!\r\n", "Within-read Skew: Position 33 from the end of reads is skewed!\r\n", "Within-read Skew: Position 34 from the end of reads is skewed!\r\n", "Within-read Skew: Position 35 from the end of reads is skewed!\r\n", "Within-read Skew: Position 36 from the end of reads is skewed!\r\n", "Within-read Skew: Position 37 from the end of reads is skewed!\r\n", "Warning: Too much skewing found (76), disabling skew clipping\r\n", "Threshold used: 751 out of 300000\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC): counted 5154 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 5\r\n", "Adapter No Hit (AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG): counted 1699 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC): counted 6822 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 4\r\n", "Adapter No Hit (GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA): counted 1672 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2136 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter No Hit (TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC): counted 2720 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 1933 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 1933 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC): counted 5154 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC): counted 6822 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2136 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 1933 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 1933 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC): counted 5154 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCC): counted 6822 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2136 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 1933 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC): counted 5154 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC): counted 6822 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2136 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 1933 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC): counted 5154 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC): counted 6822 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2136 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 1933 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC): counted 5154 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC): counted 6822 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2136 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 1933 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 1933 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 9 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC): counted 5154 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2136 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 6\r\n", "Adapter No Hit (AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG): counted 1699 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 6\r\n", "Adapter No Hit (GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA): counted 1672 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC): counted 6822 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC): counted 5154 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 5\r\n", "Adapter No Hit (TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC): counted 2720 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC): counted 5154 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC): counted 6822 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC): counted 5154 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC): counted 5154 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC): counted 6822 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC): counted 5154 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC): counted 6822 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC): counted 5154 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC): counted 6822 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 9 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATG): counted 5154 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq', clip set to 5\r\n", "Files: 2\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Total reads: 8297202\r\n", "Too short after clip: 273559\r\n", "Clipped 'start' reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq): Count 19291, Mean: 6.69, Sd: 8.01\r\n", "Clipped 'end' reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq): Count 162366, Mean: 18.88, Sd: 14.83\r\n", "Trimmed 749148 reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq) by an average of 11.48 bases on quality < 7\r\n", "Clipped 'end' reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq): Count 158664, Mean: 17.93, Sd: 13.92\r\n", "Trimmed 4912567 reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq) by an average of 10.92 bases on quality < 7\r\n" ] } ], "prompt_number": 15 }, { "cell_type": "code", "collapsed": false, "input": [ "#variables\n", "lib=\"M3\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 16 }, { "cell_type": "code", "collapsed": false, "input": [ "!/Volumes/Bay3/Software/ea-utils.1.1.2-537/fastq-mcf \\\n", "-o /Volumes/web/cnidarian/mcf_{lib}_R1.fastq \\\n", "-o /Volumes/web/cnidarian/mcf_{lib}_R2.fastq \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Adapters_LarvaeSequencingFiles.txt \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/{lib}_R1.fastq \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/{lib}_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": [ "Warning: Too much skewing found (76), disabling skew clipping\r\n", "Threshold used: 751 out of 300000\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC): counted 3237 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter No Hit (AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG): counted 1851 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC): counted 5462 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter No Hit (GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA): counted 1816 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 3177 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter No Hit (TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC): counted 2878 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2880 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 2880 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC): counted 3237 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC): counted 5462 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 3177 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2880 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 2880 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC): counted 3237 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCC): counted 5462 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 3177 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2880 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC): counted 3237 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC): counted 5462 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 3177 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2880 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC): counted 3237 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC): counted 5462 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 3177 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2880 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC): counted 3237 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC): counted 5462 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 3177 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2880 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 2880 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 9 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC): counted 3237 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 3177 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter No Hit (AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG): counted 1851 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 6\r\n", "Adapter No Hit (GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA): counted 1816 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC): counted 5462 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC): counted 3237 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter No Hit (TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC): counted 2878 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC): counted 3237 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC): counted 5462 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC): counted 3237 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC): counted 3237 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC): counted 5462 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC): counted 3237 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC): counted 5462 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC): counted 3237 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC): counted 5462 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 9 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATG): counted 3237 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq', clip set to 5\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Files: 2\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Total reads: 8078115\r\n", "Too short after clip: 210991\r\n", "Clipped 'end' reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq): Count 202159, Mean: 18.74, Sd: 14.05\r\n", "Trimmed 680382 reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq) by an average of 11.74 bases on quality < 7\r\n", "Clipped 'end' reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq): Count 205913, Mean: 16.97, Sd: 13.53\r\n", "Trimmed 4893990 reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq) by an average of 10.93 bases on quality < 7\r\n" ] } ], "prompt_number": 17 }, { "cell_type": "code", "collapsed": false, "input": [ "#variables\n", "lib=\"T1D3\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 18 }, { "cell_type": "code", "collapsed": false, "input": [ "!/Volumes/Bay3/Software/ea-utils.1.1.2-537/fastq-mcf \\\n", "-o /Volumes/web/cnidarian/mcf_{lib}_R1.fastq \\\n", "-o /Volumes/web/cnidarian/mcf_{lib}_R2.fastq \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Adapters_LarvaeSequencingFiles.txt \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/{lib}_R1.fastq \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/{lib}_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 19 from the start of reads is skewed!\r\n", "Within-read Skew: Position 20 from the start of reads is skewed!\r\n", "Within-read Skew: Position 21 from the start of reads is skewed!\r\n", "Within-read Skew: Position 22 from the start of reads is skewed!\r\n", "Within-read Skew: Position 24 from the start of reads is skewed!\r\n", "Within-read Skew: Position 27 from the start of reads is skewed!\r\n", "Within-read Skew: Position 28 from the start of reads is skewed!\r\n", "Within-read Skew: Position 29 from the start of reads is skewed!\r\n", "Within-read Skew: Position 31 from the start of reads is skewed!\r\n", "Within-read Skew: Position 33 from the start of reads is skewed!\r\n", "Within-read Skew: Position 34 from the start of reads is skewed!\r\n", "Within-read Skew: Position 35 from the start of reads is skewed!\r\n", "Within-read Skew: Position 17 from the end of reads is skewed!\r\n", "Within-read Skew: Position 18 from the end of reads is skewed!\r\n", "Within-read Skew: Position 20 from the end of reads is skewed!\r\n", "Within-read Skew: Position 21 from the end of reads is skewed!\r\n", "Within-read Skew: Position 23 from the end of reads is skewed!\r\n", "Within-read Skew: Position 24 from the end of reads is skewed!\r\n", "Within-read Skew: Position 27 from the end of reads is skewed!\r\n", "Within-read Skew: Position 28 from the end of reads is skewed!\r\n", "Within-read Skew: Position 29 from the end of reads is skewed!\r\n", "Within-read Skew: Position 30 from the end of reads is skewed!\r\n", "Within-read Skew: Position 31 from the end of reads is skewed!\r\n", "Within-read Skew: Position 33 from the end of reads is skewed!\r\n", "Within-read Skew: Position 35 from the end of reads is skewed!\r\n", "Within-read Skew: Position 36 from the end of reads is skewed!\r\n", "Within-read Skew: Position 37 from the end of reads is skewed!\r\n", "Within-read Skew: Position 1 from the end of reads is skewed!\r\n", "Within-read Skew: Position 2 from the end of reads is skewed!\r\n", "Within-read Skew: Position 3 from the end of reads is skewed!\r\n", "Within-read Skew: Position 4 from the end of reads is skewed!\r\n", "Within-read Skew: Position 5 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 9 from the end of reads is skewed!\r\n", "Within-read Skew: Position 10 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 12 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", "Within-read Skew: Position 17 from the end of reads is skewed!\r\n", "Within-read Skew: Position 18 from the end of reads is skewed!\r\n", "Within-read Skew: Position 19 from the end of reads is skewed!\r\n", "Within-read Skew: Position 20 from the end of reads is skewed!\r\n", "Within-read Skew: Position 21 from the end of reads is skewed!\r\n", "Within-read Skew: Position 22 from the end of reads is skewed!\r\n", "Within-read Skew: Position 23 from the end of reads is skewed!\r\n", "Within-read Skew: Position 24 from the end of reads is skewed!\r\n", "Within-read Skew: Position 25 from the end of reads is skewed!\r\n", "Within-read Skew: Position 26 from the end of reads is skewed!\r\n", "Within-read Skew: Position 27 from the end of reads is skewed!\r\n", "Within-read Skew: Position 28 from the end of reads is skewed!\r\n", "Within-read Skew: Position 29 from the end of reads is skewed!\r\n", "Within-read Skew: Position 30 from the end of reads is skewed!\r\n", "Within-read Skew: Position 31 from the end of reads is skewed!\r\n", "Within-read Skew: Position 32 from the end of reads is skewed!\r\n", "Within-read Skew: Position 33 from the end of reads is skewed!\r\n", "Within-read Skew: Position 34 from the end of reads is skewed!\r\n", "Within-read Skew: Position 35 from the end of reads is skewed!\r\n", "Within-read Skew: Position 36 from the end of reads is skewed!\r\n", "Within-read Skew: Position 37 from the end of reads is skewed!\r\n", "Trim 'start': 3 from /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq\r\n", "Trim 'end': 16 from /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq\r\n", "Trim 'start': 38 from /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq\r\n", "Threshold used: 751 out of 300000\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC): counted 4411 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 5\r\n", "Adapter No Hit (AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG): counted 1581 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC): counted 9162 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 4\r\n", "Adapter No Hit (GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA): counted 1542 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 4300 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter No Hit (TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC): counted 2560 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 3898 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 3898 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC): counted 4411 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC): counted 9162 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 4300 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 3898 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 3898 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC): counted 4411 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCC): counted 9162 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 4300 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 3898 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC): counted 4411 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC): counted 9162 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 4300 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 3898 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC): counted 4411 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC): counted 9162 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 4300 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 3898 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC): counted 4411 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC): counted 9162 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 4300 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 3898 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 3898 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 9 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC): counted 4411 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 4300 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 5\r\n", "Adapter No Hit (AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG): counted 1581 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 6\r\n", "Adapter No Hit (GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA): counted 1542 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC): counted 9162 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC): counted 4411 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 5\r\n", "Adapter No Hit (TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC): counted 2560 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC): counted 4411 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC): counted 9162 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC): counted 4411 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC): counted 4411 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC): counted 9162 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC): counted 4411 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC): counted 9162 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC): counted 4411 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC): counted 9162 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 9 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATG): counted 4411 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq', clip set to 5\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Files: 2\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Total reads: 5465974\r\n", "Too short after clip: 449574\r\n", "Clipped 'end' reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq): Count 166326, Mean: 16.63, Sd: 12.16\r\n", "Trimmed 113807 reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq) by an average of 17.38 bases on quality < 7\r\n", "Clipped 'end' reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq): Count 100612, Mean: 10.09, Sd: 3.88\r\n", "Trimmed 2999841 reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq) by an average of 11.91 bases on quality < 7\r\n" ] } ], "prompt_number": 19 }, { "cell_type": "code", "collapsed": false, "input": [ "#variables\n", "lib=\"T1D5\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 20 }, { "cell_type": "code", "collapsed": false, "input": [ "!/Volumes/Bay3/Software/ea-utils.1.1.2-537/fastq-mcf \\\n", "-o /Volumes/web/cnidarian/mcf_{lib}_R1.fastq \\\n", "-o /Volumes/web/cnidarian/mcf_{lib}_R2.fastq \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Adapters_LarvaeSequencingFiles.txt \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/{lib}_R1.fastq \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/{lib}_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": [ "Warning: Too much skewing found (76), disabling skew clipping\r\n", "Threshold used: 751 out of 300000\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC): counted 2948 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter No Hit (AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG): counted 1107 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 7\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC): counted 4607 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter No Hit (GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA): counted 1081 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 7\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2851 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 5\r\n", "Adapter No Hit (TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC): counted 1910 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2562 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 2562 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC): counted 2948 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC): counted 4607 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2851 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2562 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 2562 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC): counted 2948 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCC): counted 4607 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2851 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2562 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC): counted 2948 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC): counted 4607 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2851 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2562 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC): counted 2948 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC): counted 4607 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2851 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2562 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC): counted 2948 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC): counted 4607 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2851 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2562 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 2562 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 9 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC): counted 2948 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2851 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 5\r\n", "Adapter No Hit (AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG): counted 1107 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 7\r\n", "Adapter No Hit (GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA): counted 1081 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 7\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC): counted 4607 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC): counted 2948 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter No Hit (TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC): counted 1910 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC): counted 2948 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC): counted 4607 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC): counted 2948 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC): counted 2948 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC): counted 4607 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC): counted 2948 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC): counted 4607 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC): counted 2948 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC): counted 4607 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 9 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATG): counted 2948 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq', clip set to 5\r\n", "Files: 2\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Total reads: 6327160\r\n", "Too short after clip: 147886\r\n", "Clipped 'end' reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq): Count 143711, Mean: 17.70, Sd: 12.45\r\n", "Trimmed 614930 reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq) by an average of 11.55 bases on quality < 7\r\n", "Clipped 'end' reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq): Count 136939, Mean: 17.47, Sd: 12.21\r\n", "Trimmed 2554684 reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq) by an average of 11.73 bases on quality < 7\r\n" ] } ], "prompt_number": 21 }, { "cell_type": "code", "collapsed": false, "input": [ "#variables\n", "lib=\"T3D3\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 22 }, { "cell_type": "code", "collapsed": false, "input": [ "!/Volumes/Bay3/Software/ea-utils.1.1.2-537/fastq-mcf \\\n", "-o /Volumes/web/cnidarian/mcf_{lib}_R1.fastq \\\n", "-o /Volumes/web/cnidarian/mcf_{lib}_R2.fastq \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Adapters_LarvaeSequencingFiles.txt \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/{lib}_R1.fastq \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/{lib}_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 19 from the start of reads is skewed!\r\n", "Within-read Skew: Position 20 from the start of reads is skewed!\r\n", "Within-read Skew: Position 21 from the start of reads is skewed!\r\n", "Within-read Skew: Position 22 from the start of reads is skewed!\r\n", "Within-read Skew: Position 24 from the start of reads is skewed!\r\n", "Within-read Skew: Position 27 from the start of reads is skewed!\r\n", "Within-read Skew: Position 28 from the start of reads is skewed!\r\n", "Within-read Skew: Position 29 from the start of reads is skewed!\r\n", "Within-read Skew: Position 31 from the start of reads is skewed!\r\n", "Within-read Skew: Position 33 from the start of reads is skewed!\r\n", "Within-read Skew: Position 36 from the start of reads is skewed!\r\n", "Within-read Skew: Position 37 from the start of reads is skewed!\r\n", "Within-read Skew: Position 17 from the end of reads is skewed!\r\n", "Within-read Skew: Position 18 from the end of reads is skewed!\r\n", "Within-read Skew: Position 20 from the end of reads is skewed!\r\n", "Within-read Skew: Position 21 from the end of reads is skewed!\r\n", "Within-read Skew: Position 23 from the end of reads is skewed!\r\n", "Within-read Skew: Position 24 from the end of reads is skewed!\r\n", "Within-read Skew: Position 27 from the end of reads is skewed!\r\n", "Within-read Skew: Position 28 from the end of reads is skewed!\r\n", "Within-read Skew: Position 29 from the end of reads is skewed!\r\n", "Within-read Skew: Position 30 from the end of reads is skewed!\r\n", "Within-read Skew: Position 31 from the end of reads is skewed!\r\n", "Within-read Skew: Position 33 from the end of reads is skewed!\r\n", "Within-read Skew: Position 35 from the end of reads is skewed!\r\n", "Within-read Skew: Position 36 from the end of reads is skewed!\r\n", "Within-read Skew: Position 37 from the end of reads is skewed!\r\n", "Within-read Skew: Position 27 from the end of reads is skewed!\r\n", "Within-read Skew: Position 28 from the end of reads is skewed!\r\n", "Within-read Skew: Position 29 from the end of reads is skewed!\r\n", "Within-read Skew: Position 30 from the end of reads is skewed!\r\n", "Within-read Skew: Position 31 from the end of reads is skewed!\r\n", "Within-read Skew: Position 32 from the end of reads is skewed!\r\n", "Within-read Skew: Position 33 from the end of reads is skewed!\r\n", "Within-read Skew: Position 34 from the end of reads is skewed!\r\n", "Within-read Skew: Position 35 from the end of reads is skewed!\r\n", "Within-read Skew: Position 36 from the end of reads is skewed!\r\n", "Within-read Skew: Position 37 from the end of reads is skewed!\r\n", "Warning: Too much skewing found (64), disabling skew clipping\r\n", "Threshold used: 751 out of 300000\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC): counted 6933 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter No Hit (AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG): counted 1409 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC): counted 9568 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter No Hit (GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA): counted 1371 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 3169 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter No Hit (TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC): counted 2497 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2903 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 2903 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC): counted 6934 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC): counted 9568 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 3169 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2903 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 2903 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC): counted 6933 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCC): counted 9568 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 3169 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2903 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC): counted 6933 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC): counted 9568 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 3169 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2903 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC): counted 6933 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC): counted 9568 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 3169 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2903 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC): counted 6933 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC): counted 9568 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 3169 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2903 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 2903 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 9 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC): counted 6933 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 3169 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 5\r\n", "Adapter No Hit (AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG): counted 1409 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 6\r\n", "Adapter No Hit (GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA): counted 1371 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC): counted 9568 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC): counted 6933 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter No Hit (TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC): counted 2497 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC): counted 6934 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC): counted 9568 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC): counted 6933 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC): counted 6933 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC): counted 9568 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC): counted 6933 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC): counted 9568 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC): counted 6933 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC): counted 9568 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 9 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATG): counted 6933 at the 'start' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq', clip set to 4\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Files: 2\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Total reads: 7380649\r\n", "Too short after clip: 270860\r\n", "Clipped 'start' reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq): Count 112025, Mean: 4.65, Sd: 4.54\r\n", "Clipped 'end' reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq): Count 164426, Mean: 16.65, Sd: 13.80\r\n", "Trimmed 647629 reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq) by an average of 10.89 bases on quality < 7\r\n", "Clipped 'end' reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq): Count 144073, Mean: 17.36, Sd: 13.18\r\n", "Trimmed 5076848 reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq) by an average of 10.78 bases on quality < 7\r\n" ] } ], "prompt_number": 23 }, { "cell_type": "code", "collapsed": false, "input": [ "#variables\n", "lib=\"T3D5\"" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 24 }, { "cell_type": "code", "collapsed": false, "input": [ "!/Volumes/Bay3/Software/ea-utils.1.1.2-537/fastq-mcf \\\n", "-o /Volumes/web/cnidarian/mcf_{lib}_R1.fastq \\\n", "-o /Volumes/web/cnidarian/mcf_{lib}_R2.fastq \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Adapters_LarvaeSequencingFiles.txt \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/{lib}_R1.fastq \\\n", "/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/{lib}_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": [ "Warning: Too much skewing found (76), disabling skew clipping\r\n", "Threshold used: 751 out of 300000\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC): counted 2626 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter No Hit (AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG): counted 1606 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC): counted 6629 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 4\r\n", "Adapter No Hit (GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA): counted 1591 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2631 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter No Hit (TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC): counted 2720 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 5\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2408 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 2408 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC): counted 2626 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC): counted 6629 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2631 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2408 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 2408 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC): counted 2626 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCC): counted 6629 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2631 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2408 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC): counted 2626 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC): counted 6629 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2631 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2408 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC): counted 2626 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC): counted 6629 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2631 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2408 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC): counted 2626 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC): counted 6629 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 4\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2631 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT): counted 2408 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (98% over 50bp) (ATCGGAAGAGCGTCGTGTAGGGAAAGAGGGTAGATCTCGGTGGTCGCCGT): counted 2408 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 9 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC): counted 2626 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter Illumina Single End PCR Primer 1 (100% over 50bp) (GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG): counted 2631 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 6\r\n", "Adapter No Hit (AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG): counted 1606 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter No Hit (GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA): counted 1591 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCC): counted 6629 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 3 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGC): counted 2626 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter No Hit (TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC): counted 2720 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq', clip set to 5\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC): counted 2626 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 6 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC): counted 6629 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 4 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC): counted 2626 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC): counted 2626 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 5 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC): counted 6629 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGC): counted 2626 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 7 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC): counted 6629 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGC): counted 2626 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n", "Adapter TruSeq Adapter, Index 8 (100% over 50bp) (ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCC): counted 6629 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 4\r\n", "Adapter TruSeq Adapter, Index 9 (100% over 50bp) (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATG): counted 2626 at the 'end' of '/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq', clip set to 6\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Files: 2\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Total reads: 7350645\r\n", "Too short after clip: 224845\r\n", "Clipped 'end' reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq): Count 171219, Mean: 18.47, Sd: 13.89\r\n", "Trimmed 683973 reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq) by an average of 11.34 bases on quality < 7\r\n", "Clipped 'end' reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq): Count 164649, Mean: 17.84, Sd: 13.46\r\n", "Trimmed 3969240 reads (/Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq) by an average of 11.14 bases on quality < 7\r\n" ] } ], "prompt_number": 25 }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }