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.