[BioC] edgeR/DESeq for ChIP-seq analysis

[Cittaro Davide]

Hi there, I'm writing to the list to have your comment about the possibility of using edgeR or DESeq for the analysis of ChIP-seq samples.
Standard approaches to ChIP-seq analysis (relying on external software such as MACS) do not make analysis of replicates easy. I've seen people looking for peaks and then compare the common/differential intervals between replicates in case/control design. I wonder if a more general approach may work (and I'm going to test this anyway...).
Since the negative binomial model stands for ChIP-seq analysis, both edgeR and DESeq should work well. One can use external software to identify regions and compute the union of all regions as it was a "gene list". From that point on, the pipeline should not differ from standard gene expression analysis.
What do you think?

d
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Davide Cittaro, PhD

Coordinator of Bioinformatics Core
Center for Translational Genomics and Bioinformatics
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Office: +39 02 26439140
Mail: cittaro.davide at hsr.it
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