{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "###Quality trim all fastq.gz files using [Trimmomatic (v0.30)](http://www.usadellab.org/cms/?page=trimmomatic)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "####Code explanation of for loop below:\n", "1. ```%%bash``` specifies to use the shell for this Jupyter cell\n", "2. ```for file in /Volumes/nightingales/C_gigas/2212_lane2_[^N]*``` initiates a for loop to handle all files beginning with ```2212_lane2_``` and only those that do not have the letter \"N\" at that position in the file name.\n", "3. ```do``` tells the for loop what to do with each of the files.\n", "4. ```newname=${file##*/}``` takes the value of the ```$file``` variable (which is ```/Volumes/nightingales/C_gigas/2212_lane2_[^N]*```) and trims the longest match from the beginning of the pattern (the pattern is ```*/```; the ```##``` is a bash command to specifiy how to trim). The resulting output (which is just the file name without the full path) is then stored in the ```newname``` variable.\n", "5. This line initiates Trimmomatic and uses the following arguments to specify order of execution:\n", " 1. single end reads (```SE```)\n", " 1. number of threads (```-threads 16```), \n", " 2. type of quality score (```-phred33```),\n", " 3. input file location (```\"$file\"```),\n", " 4. output file name/location (```/Volumes/Data/Sam/scratch/20140414_trimmed_$newname```),\n", " 5. single end Illumina TruSeq adaptor trimming (```ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10```),\n", " 6. cut number of bases at beginning of read if below quality threshold (```LEADING:3```)\n", " 7. cut number of bases at end of read if below quality threshold (```TRAILING:3```)\n", " 8. cut if average quality within 4 base window falls below 15 (```SLIDINGWINDOW:4:15```)\n", "6. ```done``` closes for loop." ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "collapsed": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_gigas/2212_lane2_CTTGTA_L002_R1_001.fastq.gz /Volumes/Data/Sam/scratch/20140414_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'\n", "ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\n", "Input Reads: 16000000 Surviving: 15922161 (99.51%) Dropped: 77839 (0.49%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_gigas/2212_lane2_CTTGTA_L002_R1_002.fastq.gz /Volumes/Data/Sam/scratch/20140414_trimmed_2212_lane2_CTTGTA_L002_R1_002.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'\n", "ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\n", "Input Reads: 16000000 Surviving: 15906198 (99.41%) Dropped: 93802 (0.59%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_gigas/2212_lane2_CTTGTA_L002_R1_003.fastq.gz /Volumes/Data/Sam/scratch/20140414_trimmed_2212_lane2_CTTGTA_L002_R1_003.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'\n", "ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\n", "Input Reads: 16000000 Surviving: 15881522 (99.26%) Dropped: 118478 (0.74%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_gigas/2212_lane2_CTTGTA_L002_R1_004.fastq.gz /Volumes/Data/Sam/scratch/20140414_trimmed_2212_lane2_CTTGTA_L002_R1_004.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'\n", "ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\n", "Input Reads: 10634369 Surviving: 10548081 (99.19%) Dropped: 86288 (0.81%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_gigas/2212_lane2_GCCAAT_L002_R1_001.fastq.gz /Volumes/Data/Sam/scratch/20140414_trimmed_2212_lane2_GCCAAT_L002_R1_001.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'\n", "ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\n", "Input Reads: 16000000 Surviving: 15956775 (99.73%) Dropped: 43225 (0.27%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_gigas/2212_lane2_GCCAAT_L002_R1_002.fastq.gz /Volumes/Data/Sam/scratch/20140414_trimmed_2212_lane2_GCCAAT_L002_R1_002.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'\n", "ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\n", "Input Reads: 16000000 Surviving: 15944342 (99.65%) Dropped: 55658 (0.35%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_gigas/2212_lane2_GCCAAT_L002_R1_003.fastq.gz /Volumes/Data/Sam/scratch/20140414_trimmed_2212_lane2_GCCAAT_L002_R1_003.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'\n", "ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\n", "Input Reads: 16000000 Surviving: 15952602 (99.70%) Dropped: 47398 (0.30%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_gigas/2212_lane2_GCCAAT_L002_R1_004.fastq.gz /Volumes/Data/Sam/scratch/20140414_trimmed_2212_lane2_GCCAAT_L002_R1_004.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'\n", "ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\n", "Input Reads: 16000000 Surviving: 15922255 (99.51%) Dropped: 77745 (0.49%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_gigas/2212_lane2_GCCAAT_L002_R1_005.fastq.gz /Volumes/Data/Sam/scratch/20140414_trimmed_2212_lane2_GCCAAT_L002_R1_005.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'\n", "ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\n", "Input Reads: 16000000 Surviving: 15909223 (99.43%) Dropped: 90777 (0.57%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_gigas/2212_lane2_GCCAAT_L002_R1_006.fastq.gz /Volumes/Data/Sam/scratch/20140414_trimmed_2212_lane2_GCCAAT_L002_R1_006.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'\n", "Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'\n", "ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences\n", "Input Reads: 255678 Surviving: 253470 (99.14%) Dropped: 2208 (0.86%)\n", "TrimmomaticSE: Completed successfully\n" ] } ], "source": [ "%%bash\n", "for file in /Volumes/nightingales/C_gigas/2212_lane2_[^N]*\n", "do\n", "newname=${file##*/}\n", "java -jar /usr/local/bioinformatics/Trimmomatic-0.30/trimmomatic-0.30.jar SE -threads 16 -phred33 \"$file\" /Volumes/Data/Sam/scratch/20140414_trimmed_$newname ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15;\n", "done" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "###FASTQC on all trimmed files using [FASTQC (v0.11.2)](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)" ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "collapsed": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Analysis complete for 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n", "Analysis complete for 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_002.fastq.gz\n", "Analysis complete for 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_003.fastq.gz\n", "Analysis complete for 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_004.fastq.gz\n", "Analysis complete for 20150414_trimmed_2212_lane2_GCCAAT_L002_R1_001.fastq.gz\n", "Analysis complete for 20150414_trimmed_2212_lane2_GCCAAT_L002_R1_002.fastq.gz\n", "Analysis complete for 20150414_trimmed_2212_lane2_GCCAAT_L002_R1_003.fastq.gz\n", "Analysis complete for 20150414_trimmed_2212_lane2_GCCAAT_L002_R1_004.fastq.gz\n", "Analysis complete for 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"/Volumes/Eagle/Arabidopsis\n" ] } ], "source": [ "cd /Volumes/Eagle/Arabidopsis/" ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Archive: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc.zip\n", " creating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/\n", " creating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Icons/\n", " creating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/\n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Icons/fastqc_icon.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Icons/warning.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Icons/error.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Icons/tick.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/summary.txt \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/per_base_quality.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/per_tile_quality.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/per_sequence_quality.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/per_base_sequence_content.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/per_sequence_gc_content.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/per_base_n_content.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/sequence_length_distribution.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/duplication_levels.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/adapter_content.png \n", " inflating: 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\n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_002_fastqc/summary.txt \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_002_fastqc/Images/per_base_quality.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_002_fastqc/Images/per_tile_quality.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_002_fastqc/Images/per_sequence_quality.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_002_fastqc/Images/per_base_sequence_content.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_002_fastqc/Images/per_sequence_gc_content.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_002_fastqc/Images/per_base_n_content.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_002_fastqc/Images/sequence_length_distribution.png \n", " inflating: 20150414_trimmed_2212_lane2_CTTGTA_L002_R1_002_fastqc/Images/duplication_levels.png \n", " inflating: 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20150414_trimmed_2212_lane2_GCCAAT_L002_R1_006_fastqc/Images/kmer_profiles.png \n", " inflating: 20150414_trimmed_2212_lane2_GCCAAT_L002_R1_006_fastqc/fastqc_report.html \n", " inflating: 20150414_trimmed_2212_lane2_GCCAAT_L002_R1_006_fastqc/fastqc_data.txt \n", " inflating: 20150414_trimmed_2212_lane2_GCCAAT_L002_R1_006_fastqc/fastqc.fo \n" ] } ], "source": [ "%%bash\n", "for file in 20150414_trimmed_2212*.zip; do unzip \"$file\"; done" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2112_lane1_ACAGTG_L001_R1_002_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", 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"20150414_trimmed_2112_lane1_CAGATC_L001_R1_002_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2112_lane1_CAGATC_L001_R1_003_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2112_lane1_GCCAAT_L001_R1_001_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2112_lane1_GCCAAT_L001_R1_002_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2112_lane1_TGACCA_L001_R1_001_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2212_lane2_CTTGTA_L002_R1_002_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2212_lane2_CTTGTA_L002_R1_003_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2212_lane2_CTTGTA_L002_R1_004_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2212_lane2_GCCAAT_L002_R1_001_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2212_lane2_GCCAAT_L002_R1_002_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2212_lane2_GCCAAT_L002_R1_003_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2212_lane2_GCCAAT_L002_R1_004_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2212_lane2_GCCAAT_L002_R1_005_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n", "\n", "20150414_trimmed_2212_lane2_GCCAAT_L002_R1_006_fastqc:\n", "\u001b[30m\u001b[43mIcons\u001b[m\u001b[m/ fastqc.fo fastqc_report.html\n", "\u001b[30m\u001b[43mImages\u001b[m\u001b[m/ fastqc_data.txt summary.txt\n" ] } ], "source": [ "ls 20150414_*fastqc" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "###Concatenate two groups of sequences into single file" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "####400ppm (control) sequences - Index GCCAAT" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/Data/Sam/scratch\n" ] } ], "source": [ "cd /Volumes/Data/Sam/scratch/" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "#gunzips all matching files in folder and appends the data to a single file:\n", "#20150414_trimmed_2212_lane2_400ppm_GCCAAT.fastq\n", "for file in 20150414_trimmed_2212_lane2_G*\n", "do\n", "gunzip -c \"$file\" >> 20150414_trimmed_2212_lane2_400ppm_GCCAAT.fastq\n", "done" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "#Gzip file\n", "gzip 20150414_trimmed_2212_lane2_400ppm_GCCAAT.fastq" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "####1000ppm (acidification) sequences - Index CTTGTA" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "#gunzips all matching files in folder and appends the data to a single file:\n", "#20150414_trimmed_2212_lane2_1000ppm_CTTGTA.fastq\n", "for file in 20150414_trimmed_2212_lane2_C*\n", "do\n", "gunzip -c \"$file\" >> 20150414_trimmed_2212_lane2_1000ppm_CTTGTA.fastq\n", "done" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "#Gzip file\n", "gzip 20150414_trimmed_2212_lane2_1000ppm_CTTGTA.fastq" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "###Copy files to Eagle for web-based access" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "for file in 2015*e2_[14]*; do cp \"$file\" /Volumes/Eagle/Arabidopsis/; done" ] } ], "metadata": { "kernelspec": { "display_name": "Python 2", "language": "python", "name": "python2" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.9" } }, "nbformat": 4, "nbformat_minor": 0 }