Question: How to find out that Chip-seq peaks falls within promoter or enhancer region of gene?
gravatar for mayurdoke
15 months ago by
mayurdoke10 wrote:


I have got the peaks and their corresponding peak regions from MACS2 peak analysis tools. I would like to know further that how can I check whether these peaks fall into enhancer or promoter region of the gene. Could you please let me know any particular software and tools available for it.

chip-seq • 1.2k views
ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson25k • written 15 months ago by mayurdoke10
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:


There are a few ways to do this. The simplest is for the bed output from MACS to be compared with a bed file of enhancer/promoter genome annotations with tools in the group Operate on Genomic Intervals.

ChIP-seq Galaxy tutorials are here and demonstrate even more downstream analysis options and tools:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson25k
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