[BioC] Using DESeq with ChIP-seq data

[Ian Donaldson]

Thank you for your reply Simon.

Just to clarify I run MACS on duplicates of the same TF at two time points:
2x TF at time point A vs control
2x TF at time point B vs control

Sorry for being slow, but i dont see how pooling all the reads will allow me to distinguish between the two time points?

Ian
________________________________________
From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] on behalf of Simon Anders [anders at embl.de]
Sent: 19 July 2011 14:57
To: bioconductor at r-project.org
Subject: Re: [BioC] Using DESeq with ChIP-seq data

Hi Ian

On 07/19/2011 02:52 PM, Ian Donaldson wrote:
 > I am planning to use DESeq to compare ChIP-seq sample binding
 > regions, but i am wondering what the best method of running DESeq
 > might be.  I have several thoughts about this, what would you
 > suggest?  The initial problem i see is that the binding regions have
 > different length coordinates and so do not initially make discrete
 > entities like gene in RNA-seq.
[...]

I assume that you used some peak finding tool to get the boundaries of
your binding regions, and that you let this tool run on each sample
separately.

I would suggest to pool the reads from all your samples and give them to
your peak finder in one big file. Any peak that is present in only one
condition will still appear in the pool (though with only half the
relative height) and for peaks appearing in both conditions, your peak
finder will report boundaries that fit some compromise shape from all
samples.


BTW, I noticed that you talk about "samples A and B". I hope you do not
intend to do a differential ChiP-Seq analysis with only one sample per
condition. Without biological replicates, you won't get any reliable
results, of course.

   Simon

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