2. Quality trimming

In the event that quality trimming is required, we recommend using the Trimmomatic software. According to MacManes (2014), light trimming of reads at or below Phred=5 scores can improve upon the final transcriptome assembly. For example purposes, simply to demonstrate the effects of trimming on this high quality data set, we'll restrict it to the high value of 36, which should remove those initial bases with quality values < 36 and we should see the results of this in a subsequent run of fastqc on the trimmed reads.

#$ -S /bin/sh
#$ -cwd
#$ -q amd.q,large.q,intel.q
#$ -l h_vmem=40G
#$ -N trimming

module load java/jdk1.7.0_40 java -jar /cm/shared/apps/trimmomatic/0.33/trimmomatic-0.33.jar PE -phred33 /ibers/ernie/scratch/userName/Fastq/clean_data/Pn_IL_l1_1.fq.gz /ibers/ernie/scratch/userName/Fastq/clean_data/Pn_IL_l1_2.fq.gz /ibers/ernie/scratch/userName/Fastq_trimmed/clean_data/Pn_IL_l1_1.fq.gz.p /ibers/ernie/scratch/userName/Fastq_trimmed/clean_data/Pn_IL_l1_1.fq.gz.unp /ibers/ernie/scratch/userName/Fastq_trimmed/clean_data/Pn_IL_l1_2.fq.gz.p /ibers/ernie/scratch/userName/Fastq_trimmed/clean_data/Pn_IL_l1_2.fq.gz.unp ILLUMINACLIP:/cm/shared/apps/trimmomatic/0.33/adapters/TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36