Question: ChIP-seq annotation, priority of the different genomic regions
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gravatar for xiangwangbio
2.7 years ago by
xiangwangbio0 wrote:

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?

chip-seq • 869 views
ADD COMMENTlink modified 2.7 years ago by Sinji2.8k • written 2.7 years ago by xiangwangbio0
1
gravatar for Sinji
2.7 years ago by
Sinji2.8k
UT Southwestern Medical Center
Sinji2.8k wrote:

I suppose it depends on your research question and what you suspect your antibody to do in your model system.

That being said, I believe that HOMER annotates peaks to their nearest TSS, thus the annotation would show the peak associated with gene A and not gene B.

ADD COMMENTlink written 2.7 years ago by Sinji2.8k

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?

ADD REPLYlink written 2.7 years ago by xiangwangbio0

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 tag bedops and Alex should be able to help you solve your question using his bedops suite.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by Sinji2.8k

Hi Sinji, I tried ChIPseeker. It works well. I really appreciate your suggestion and help!

ADD REPLYlink written 2.7 years ago by xiangwangbio0
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