Difference between revisions of "1. Read Quality Assessment"
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Running FASTQC on the raw reads: | Running FASTQC on the raw reads: | ||
| + | |||
| + | Use the following sge script: | ||
#$ -S /bin/sh | #$ -S /bin/sh | ||
#$ -cwd | #$ -cwd | ||
| − | + | #$ -q amd.q,large.q,intel.q | |
| − | + | #$ -l h_vmem=40G | |
| − | |||
module load fastqc/0.11.2 | module load fastqc/0.11.2 | ||
| − | |||
FILES=/ibers/ernie/scratch/userName/Fastq_RAW/*_4.fq.gz | FILES=/ibers/ernie/scratch/userName/Fastq_RAW/*_4.fq.gz | ||
| − | |||
for f in $FILES | for f in $FILES | ||
do | do | ||
fastqc $f | fastqc $f | ||
done | done | ||
| + | |||
| + | This generates an html file for each library containing views into the quality of the reads. You can view the results in your favourite web browser. | ||
Latest revision as of 14:11, 6 March 2017
Running FASTQC on the raw reads:
Use the following sge script:
#$ -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.
