[BioC] Using DESeq with ChIP-seq data

Simon Anders anders at embl.de
Wed Jul 20 15:20:39 CEST 2011

Hi Ian

On 07/20/2011 02:18 PM, Simon Anders wrote:
> What I meant is: Pool all four samples, give them to the peak finder in
> one big chunk and so get a list of binding regions. Then, count for each
> sample how many reads fall into each of the binding regions, obtaining a
> table with four columns for your four samples and one row for each
> binding region found in the pool. Give this table to DESeq. We've tried
> this approach once with some Pol-II ChIP-Seq data and it worked quite well.

Forgot to mention: When we did this, we counted the reads from the 
ChIPed sample. We used the input control samples only for the peak 
finding, not in the counting. IIRC, we only had one common control lane 
for both conditions, so that it would cancel out when comparing the 

If you have separate controls, you may want to count for them as well 
and use DESeq's GLM function to test for an interaction contrast.


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