Difference between revisions of "1. Read Quality Assessment"
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fastqc $f | fastqc $f | ||
done | done | ||
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| + | This generates an html file for each library containing views into the quality of the reads. You can view the results in your favourite web browser. | ||
Revision as of 14:10, 6 March 2017
Running FASTQC on the raw reads:
#$ -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.
