{ "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_virginica/2112_lane1_[^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 (```\"$file\"```),\n", " 4. output file name/location (```/Volumes/Data/Sam/scratch/20150414_trimmed_$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": 2, "metadata": { "collapsed": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_ACAGTG_L001_R1_001.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_ACAGTG_L001_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: 11370712 (71.07%) Dropped: 4629288 (28.93%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_ACAGTG_L001_R1_002.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_ACAGTG_L001_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: 1327210 Surviving: 889732 (67.04%) Dropped: 437478 (32.96%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_ATCACG_L001_R1_001.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_ATCACG_L001_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: 13657433 (85.36%) Dropped: 2342567 (14.64%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_ATCACG_L001_R1_002.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_ATCACG_L001_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: 13551447 (84.70%) Dropped: 2448553 (15.30%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_ATCACG_L001_R1_003.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_ATCACG_L001_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: 1409414 Surviving: 1173081 (83.23%) Dropped: 236333 (16.77%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_CAGATC_L001_R1_001.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_CAGATC_L001_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: 12742235 (79.64%) Dropped: 3257765 (20.36%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_CAGATC_L001_R1_002.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_CAGATC_L001_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: 12468557 (77.93%) Dropped: 3531443 (22.07%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_CAGATC_L001_R1_003.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_CAGATC_L001_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: 7780221 Surviving: 6056165 (77.84%) Dropped: 1724056 (22.16%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_GCCAAT_L001_R1_001.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_GCCAAT_L001_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: 13494573 (84.34%) Dropped: 2505427 (15.66%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_GCCAAT_L001_R1_002.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_GCCAAT_L001_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: 8792684 Surviving: 7316692 (83.21%) Dropped: 1475992 (16.79%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_TGACCA_L001_R1_001.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_TGACCA_L001_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: 9188940 Surviving: 2827107 (30.77%) Dropped: 6361833 (69.23%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_TTAGGC_L001_R1_001.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_TTAGGC_L001_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: 13428815 (83.93%) Dropped: 2571185 (16.07%)\n", "TrimmomaticSE: Completed successfully\n", "TrimmomaticSE: Started with arguments: -threads 16 -phred33 /Volumes/nightingales/C_virginica/2112_lane1_TTAGGC_L001_R1_002.fastq.gz /Volumes/Data/Sam/scratch/20150414_trimmed_2112_lane1_TTAGGC_L001_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: 9752634 Surviving: 8034025 (82.38%) Dropped: 1718609 (17.62%)\n", "TrimmomaticSE: Completed successfully\n" ] } ], "source": [ "%%bash\n", "for file in /Volumes/nightingales/C_virginica/2112_lane1_[^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/20150414_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": 23, "metadata": { "collapsed": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Analysis complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz\n", "Analysis complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_002.fastq.gz\n", "Analysis complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_001.fastq.gz\n", "Analysis complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_002.fastq.gz\n", "Analysis complete for 20150414_trimmed_2112_lane1_ATCACG_L001_R1_003.fastq.gz\n", "Analysis complete for 20150414_trimmed_2112_lane1_CAGATC_L001_R1_001.fastq.gz\n", "Analysis complete for 20150414_trimmed_2112_lane1_CAGATC_L001_R1_002.fastq.gz\n", "Analysis complete for 20150414_trimmed_2112_lane1_CAGATC_L001_R1_003.fastq.gz\n", "Analysis complete for 20150414_trimmed_2112_lane1_GCCAAT_L001_R1_001.fastq.gz\n", "Analysis complete for 20150414_trimmed_2112_lane1_GCCAAT_L001_R1_002.fastq.gz\n", "Analysis complete for 20150414_trimmed_2112_lane1_TGACCA_L001_R1_001.fastq.gz\n", "Analysis complete for 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_001.fastq.gz\n", "Analysis complete for 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002.fastq.gz\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started analysis of 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz\n", "Approx 5% complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz\n", "Approx 10% complete for 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001.fastq.gz\n", "Approx 15% complete for 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"stdout", "output_type": "stream", "text": [ "Archive: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc.zip\n", " creating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/\n", " creating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Icons/\n", " creating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Images/\n", " inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Icons/fastqc_icon.png \n", " inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Icons/warning.png \n", " inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Icons/error.png \n", " inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Icons/tick.png \n", " inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/summary.txt \n", " inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Images/per_base_quality.png \n", " inflating: 20150414_trimmed_2112_lane1_ACAGTG_L001_R1_001_fastqc/Images/per_tile_quality.png \n", " inflating: 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\n", " inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/summary.txt \n", " inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/per_base_quality.png \n", " inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/per_tile_quality.png \n", " inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/per_sequence_quality.png \n", " inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/per_base_sequence_content.png \n", " inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/per_sequence_gc_content.png \n", " inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/per_base_n_content.png \n", " inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/sequence_length_distribution.png \n", " inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/duplication_levels.png \n", " inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/adapter_content.png \n", " inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/Images/kmer_profiles.png \n", " inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/fastqc_report.html \n", " inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/fastqc_data.txt \n", " inflating: 20150414_trimmed_2112_lane1_TTAGGC_L001_R1_002_fastqc/fastqc.fo \n" ] } ], "source": [ "%%bash\n", "for file in 20150414_trimmed_2112_lane1_*.zip; do unzip \"$file\"; done" ] }, { "cell_type": "markdown", "metadata": { "collapsed": true }, "source": [ "###Concatenate groups of sequences into single files" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/Data/Sam/scratch\n" ] } ], "source": [ "cd /Volumes/Data/Sam/scratch/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "####HB2 \t25,000ppm oil \tIndex - ATCACG" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "#gunzips all matching files in folder and appends the data to a single file:\n", "#20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq\n", "for file in 20150414_trimmed_2112_lane1_ATCACG*\n", "do\n", "gunzip -c \"$file\" >> 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq\n", "done" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "#Gzip file\n", "gzip 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "####HB16 \t25,000ppm oil \tIndex - TTAGGC" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "#gunzips all matching files in folder and appends the data to a single file:\n", "#20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq\n", "for file in 20150414_trimmed_2112_lane1_TTAGGC*\n", "do\n", "gunzip -c \"$file\" >> 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq\n", "done" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "#Gzip file\n", "gzip 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "####HB30 \t25,000ppm oil \tIndex - TGACCA" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "#gunzips all matching files in folder and appends the data to a single file:\n", "#20150414_trimmed_2112_lane1_HB30_Oil_25000ppm_TGACCA.fastq\n", "for file in 20150414_trimmed_2112_lane1_TGACCA*\n", "do\n", "gunzip -c \"$file\" >> 20150414_trimmed_2112_lane1_HB30_Oil_25000ppm_TGACCA.fastq\n", "done" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "#Gzip file\n", "gzip 20150414_trimmed_2112_lane1_HB30_Oil_25000ppm_TGACCA.fastq" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "####NB3 \tNo oil \tIndex - ACAGTG" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "#gunzips all matching files in folder and appends the data to a single file:\n", "#20150414_trimmed_2112_lane1_NB3_NoOil_ACAGTG.fastq\n", "for file in 20150414_trimmed_2112_lane1_ACAGTG*\n", "do\n", "gunzip -c \"$file\" >> 20150414_trimmed_2112_lane1_NB3_NoOil_ACAGTG.fastq\n", "done" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "#Gzip file\n", "gzip 20150414_trimmed_2112_lane1_NB3_NoOil_ACAGTG.fastq" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "####NB6 \tNo oil \tIndex - GCCAAT" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "#gunzips all matching files in folder and appends the data to a single file:\n", "#20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq\n", "for file in 20150414_trimmed_2112_lane1_GCCAAT*\n", "do\n", "gunzip -c \"$file\" >> 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq\n", "done" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "#Gzip file\n", "gzip 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "####NB11 \tNo oil \tIndex - CAGATC" ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "#gunzips all matching files in folder and appends the data to a single file:\n", "#20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq\n", "for file in 20150414_trimmed_2112_lane1_CAGATC*\n", "do\n", "gunzip -c \"$file\" >> 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq\n", "done" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "#Gzip file\n", "gzip 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "###Copy files to Eagle for web-based access" ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "for file in 2015*e1_[NH]B*; do cp \"$file\" /Volumes/Eagle/Arabidopsis/; done" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 2", "language": "python", "name": "python2" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.9" } }, "nbformat": 4, "nbformat_minor": 0 }