[BioC] Using DESeq with ChIP-seq data - all or non-redundant reads?

[Ian Donaldson]

I have been using DESeq to look at differential binding in ChIP-seq for a while now.  But recently we have been discussing locally whether the ChIP-seq reads used in DESeq should be the full or non-redundant set?  There is a worry that the full set of reads may contain spuriously amplified reads, but then using a non-redundant set remove information, i.e. particularly enriched binding regions.

I would be very interested to get your views on this.

Thanks!

Ian
________________________________________
From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] on behalf of Simon Anders [anders at embl.de]
Sent: 20 July 2011 14:20
To: bioconductor at r-project.org
Subject: Re: [BioC] Using DESeq with ChIP-seq data

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
conditions.

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.

   S

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