I have DNA sample from 5 pools, having 25 fastq files each. I am running cutadapt to remove the primers using this command
cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG A7_S7_R1_001.fastq -o sb_A7_S7_R1_001.fastq --discard-untrimmed
However, this is too time consuming. I tried my hand at writing shell script
for file in /dir/*
do
cmd cutadapt -g ACTTAAGTGTATGTAAACTTCCGACTTCAACTG "$file" >> results.out
done
But it is not running . Can someone help. Thanks
cmd
in there. Put andls
in just to see which files are seen. $\endgroup$