CHIPSEQ Analysis , DiffBind Parameters

Question

[DINESHR]

Hello,

Regarding Diffbind, How does diffbind calculate common peaks with the samples. I'm observing that certain peaks identified as common using bedtools intersect are not appearing in the output report file generated after DiffBind analysis

Command used to write the file : res_deseq <- dba.report(dbObj_analyze,th=1, method=DBA_EDGER,bCalled=TRUE)

Any comment or suggestion would be highly appreciated, either about my approach with DiffBind or recommending other tools.

Thanks in advance!

Answer 1

[Rory Stark]

I assume you are checking for called peaks that overlap consensus peaks (and not the exact peaks)?

Overlapping peaks are first merged to form wider intervals that cove the whole area. By default, peaks that overlap in any two samples are kept. When counting reads, by default the point in each peak the the greatest enrichment across all samples the peak is called in is calculated, and the peak re-centered around that point and set to a pre-defined width (default 401bp). If you had a lot of peak merging, forming very wide peaks, this last re-centering step can result is a lot of the called peak areas being trimmed. You can prevent this from happening by setting summits=FALSE.