[BioC] Using DESeq with ChIP-seq data

[Simon Anders]

Hi Ian,

On 07/20/2011 10:27 AM, Ian Donaldson wrote:
> 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?

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.

An important issue here is, by the way, the width of the binding 
regions: you will have noticed that some peak finding tools report wide 
intervals, including the tails of the peaks, and others report narrow 
intervals which only include those parts of the peaks that are high. 
This can strongly influence the power of the method, as too wide regions 
dilute the signal.

Cheers
   Simon