Hej,
I am performing ChIP-seq experiments. I am looking for a program that can compare 3 groups (3 genotypes, 5 samples each). As far as I can find in the literature, the most you can compare is 2 groups.
Thank you,
Anandhakumar Chandran
I hope this may help u...
http://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf
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Matthew James Bush
In terms of genome browsers to compare multiple data sets, I use IGB:
http://bioviz.org/igb/
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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.
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