1. Read Quality Assessment

Running FASTQC on the raw reads:

Use the following sge script:

#$ -S /bin/sh
#$ -cwd
#$ -q amd.q,large.q,intel.q
#$ -l h_vmem=40G
module load fastqc/0.11.2
FILES=/ibers/ernie/scratch/userName/Fastq_RAW/*_4.fq.gz
for f in $FILES
     do
           fastqc $f
     done

This generates an html file for each library containing views into the quality of the reads. You can view the results in your favourite web browser.