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7.5 years ago
xiangwangbio
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0
I am using Homer to perform peak annotation. I am little confused about the priority of the different genomic regions.
If one peak localizes at promoter for A gene and gene body for B, which annotation is more reasonable, promoter A or gene body B?
Thanks a lot Sinji! My antibody has both promoter and gene body distribution. So maybe I should try different way. HOMER annotates peaks to their nearest TSS. Do you know any other package using different strategy?
You may be able to check out the Bioconductor package ChIPseeker, it might be able to do what you want, though I'm not entirely sure.
The way I would do this is use something like
bedtools closest
and include more than 1 annotation per peak. So for instance you would want to include both gene A and gene B because your peak overlaps regions of both.If bedtools doesn't do what you want, look into the
bedops
suite and then repost this question with the tagbedops
and Alex should be able to help you solve your question using his bedops suite.Hi Sinji, I tried ChIPseeker. It works well. I really appreciate your suggestion and help!