[BioC] DESeq on CCAT identified chipseq peaks

Simon Anders anders at embl.de
Thu May 15 11:35:40 CEST 2014


Hi Aditi

on Wed May 14 18:16:36 CEST 2014 Aditi [guest] guest at bioconductor.org
wrote:
[...]
Thus to create a unified list of peak regions and their read counts
would you suggest -
>>
>> A. Taking a union of all the CCAT called peaks and calculating read
>> count in each biological replicate OR
>>
>> B. Calculating the read count for each peak in each replicate
>> whether or not it has been called in the replicate or not
>>
>> I saw both being suggested earlier online and I am not sure which
>> is appropriate.

Both approaches will give statistically valid results. I don't have much
experience with ChIP-Seq myself, so I suggest to follow Rory's advice
(and the DiffBind vignette) to get most inferential power.

>> 2. Since this is chipseq and not rna seq data, do you agree that
>> using coverageBed ( coverageBed -abam $bamfile  -b $CCATpeaks >
>> countdata) would work as > good as HTseqcount ?

Yes. As the features do not overlap, this should not make a difference. 
BEDtools might be easier to use here, as you probably have the peaks in 
BED format, anyway. Or you use Rory's DiffBind package.

   Simon



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