bowtie2; using for multiple fastq files, linux loop code
Hi,
I’m pretty new to linux and ChipSeq analysis. At this point, I have 100 fastq.gz files to be aligned with hg19.
I already indexed my genome and called it hg19 and could align my reads individually with it but I need to have a loop to work on all the 100 files at the same time.
Can please someone help me writing the correct code for it? I see in places people using for loop but I can’t make it work for me.
My fastq files are in: /mnt/d/Chipseq/Hchipseq
This is the code I use.
for i in /mnt/d/Chipseq/Hchipseq/*.fastq
do
bowtie2 -p 16 --fast-local --no-mixed -t -x hg19 -U /mnt/d/Chipseq/Hchipseq/*.fastq S- i.sam
done
Thanks a lot for your help.
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