{
"cells": [
{
"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": "markdown",
"metadata": {},
"source": [
"###Quality trim & remove first 39bp from single FASTQ file"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Code explanation:\n",
"\n",
" java -jar /usr/local/bioinformatics/Trimmomatic-0.30/trimmomatic-0.30.jar\n",
"This line above initiates Trimmomatic and uses the following arguments to specify order of execution:\n",
"\n",
"-single end reads (SE)\n",
" \n",
"-number of threads (-threads 16),\n",
" \n",
"-type of quality score (-phred33),\n",
"\n",
"-input file location (/Volumes/nightingales/C_gigas/2212_lane2_CTTGTA_L002_R1_001.fastq.gz),\n",
"\n",
"-output file name/location (20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz),\n",
"\n",
"-single end Illumina TruSeq adaptor trimming (ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10),\n",
"\n",
"-cut number of bases at beginning of each read (HEADCROP:39)\n",
"\n",
"-cut number of bases at beginning of read if below quality threshold (LEADING:3)\n",
"\n",
"-cut number of bases at end of read if below quality threshold (TRAILING:3)\n",
"\n",
"-cut if average quality within 4 base window falls below 15 (SLIDINGWINDOW:4:15)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false
},
"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/20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 HEADCROP:39 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: 15796545 (98.73%) Dropped: 203455 (1.27%)\n",
"TrimmomaticSE: Completed successfully\n"
]
}
],
"source": [
"%%bash\n",
"java -jar /usr/local/bioinformatics/Trimmomatic-0.30/trimmomatic-0.30.jar \\\n",
"SE \\\n",
"-threads 16 \\\n",
"-phred33 \\\n",
"/Volumes/nightingales/C_gigas/2212_lane2_CTTGTA_L002_R1_001.fastq.gz \\\n",
"/Volumes/Data/Sam/scratch/20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz \\\n",
"ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 \\\n",
"HEADCROP:39 \\\n",
"LEADING:3 \\\n",
"TRAILING:3 \\\n",
"SLIDINGWINDOW:4:15"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"###FASTQC on trimmed file"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Analysis complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Started analysis of 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 5% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 10% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 15% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 20% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 25% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 30% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 35% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 40% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 45% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 50% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 55% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 60% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 65% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 70% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 75% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 80% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 85% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 90% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n",
"Approx 95% complete for 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz\n"
]
}
],
"source": [
"%%bash\n",
"fastqc /Volumes/Data/Sam/scratch/20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz \\\n",
"--outdir=/Volumes/Eagle/Arabidopsis/"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"###Copy files to Eagle for web-based access"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"cp 20150506_* /Volumes/Eagle/Arabidopsis/"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"###Unzip FASTQC output"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Archive: /Volumes/Eagle/Arabidopsis/20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc.zip\n",
" creating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/\n",
" creating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Icons/\n",
" creating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/\n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Icons/fastqc_icon.png \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Icons/warning.png \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Icons/error.png \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Icons/tick.png \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/summary.txt \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/per_base_quality.png \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/per_tile_quality.png \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/per_sequence_quality.png \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/per_base_sequence_content.png \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/per_sequence_gc_content.png \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/per_base_n_content.png \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/sequence_length_distribution.png \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/duplication_levels.png \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/adapter_content.png \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/Images/kmer_profiles.png \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/fastqc_report.html \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/fastqc_data.txt \n",
" inflating: 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/fastqc.fo \n"
]
}
],
"source": [
"%%bash\n",
"unzip /Volumes/Eagle/Arabidopsis/20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc.zip"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"###Move unzipped folder to Eagle"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"%%bash\n",
"mv 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/ /Volumes/Eagle/Arabidopsis/"
]
}
],
"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
}