Question: High Confidence Peaks From A Set Of Replicates
gravatar for ChIP
7.0 years ago by
ChIP550 wrote:


I have a set of peaks (4 replicates) and I want to find out how many of the peaks overlapping are high confidence peaks in all replicates.

The peaks that are present in all 4 replicates account for 9000 peaks, obviously they have different p-values (from macs2).

What I intend to know is that, how many of these 9000 peaks are more significantly called in all 4 replicates than compared to other peaks ( a kind of ranking system, where I can say that the top 7000 peaks out of 9000 have X pvalue or correlation in all 4 replicates).

Any suggestions?????

Thank you

chip-seq peak-calling • 2.2k views
ADD COMMENTlink modified 7.0 years ago by Dataminer2.7k • written 7.0 years ago by ChIP550

I would look for number of 9000 peaks encompassing peak summits from all replicates.

ADD REPLYlink modified 7.0 years ago • written 7.0 years ago by Dataminer2.7k
gravatar for Ryan Dale
7.0 years ago by
Ryan Dale4.9k
Bethesda, MD
Ryan Dale4.9k wrote:

Take a look at ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia -- in particular the irreproducible discovery rate (IDR) metric.

You can find some practical info on IDR at and more rigorous treatment of it in the PDFs at

ADD COMMENTlink written 7.0 years ago by Ryan Dale4.9k
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