Is there a program to analyse ChIP-seq data comparing 3 groups?

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Anandhakumar Chandran

I hope this may help u...

http://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf

Matthew James Bush

In terms of genome browsers to compare multiple data sets, I use IGB:

http://bioviz.org/igb/

Ning-Yi Shao

It depends your story. For a preliminary investigation, I would suggest you do some pair wise comparisons by utilities like diffReps, etc firstly, then use other methods like ngs.plot to cluster and group the patterns of the differential enrichment on the merged bed files of differential sites detected by the first step.