Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me3)?

Question

[hiroyuki.kato.911]

Hi,

I have called ChIP-seq broadpeak (H3K9me3, H3K27me3) using SICER2 in mm10. The peak looks good and consistent with the IGV findings.

Is there any good tools to annotate these broad peaks to coding genes?

I know GREAT(http://great.stanford.edu/public/html/) is a wonderful tool for narrow peak annotation such as ATAC or H3K27ac.

Since broad peaks span across multiple genes or gene deserts, I was wondering any standard way to annotate these peaks.

Any suggestion, or some example reference paper will also be helpful.

Thank you very much in advance.

Best,

[Matthias Zepper]

In my perception, there should be little difference between narrow peak annotation and broad peak annotation? I and others have used Homer's annotatePeaks for narrow peaks, H3K4me3 buffer domains as well as Hi-C fragments spanning multiple genes. You can also use bedtools intersect and use the -F/-f/-r parameters to restrict the overlaps.

[hiroyuki.kato.911]

Hi Matthias,

Thank you for your comments. Yes, I know annotatePeaks and bedtools intersect.

My questions is not about how to call peaks, but about how to interpret to gene or gene set annotation (Ontology or Pathways).

Thanks.

[Marco Pannone]

I would use annotatePeaks to annotate peaks to nearby genes, then use that list of genes as input to an over-representation analysis (ORA), which you can for example easily run on WebGestalt.

[hiroyuki.kato.911]

Thanks! I got it!