I have previously used DESeq to analyse differential binding in ChIP-seq data (2 replicates of two ChIP samples).  I believe the newer versions of DESeq (i have 1.6.1) are able to consider the matching input samples to correct for the background reads.

Does anyone have experience of including the background (input) reads in a DESeq analysis?  I am afraid i am not sure how to proceed using the vignette.  Is there are ChIP-seq workflow anywhere?

Thanks!
Ian



	[[alternative HTML version deleted]]

