[BioC] Using DESeq with ChIP-seq data

[Simon Anders]

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