Tool for finding peaks from Chip-seq data at multiple regions.

Question

[sangram_keshari]

I have Chip-seq information for a list of TFs. Want to find significant peaks at upstream 500bp of multiple promoter regions. Now I know one can individually look the peaks in a genome browser and confirm out. But this is a hell lot of task.

So, I want to know if is there any tool specifically designed for this task?

This will be very helpful if anyone can let me know. Thank you.

Answer 1

[Satyajeet Khare]

You can use annotatePeaks.pl from HOMER. You just need to provide the genome fasta file with gene gtf file along with the bed file of your ChIP-Seq peaks.