Irreproducibility Discovery Rate for broad histone marks.

Question

[tsomakiank]

Hello, I have to run the idr framework on some .broadPeak files. Is it appropriate to run idr on broad peaks or the framework only applies to narrow marks? Thanks in advance!

Answer 1

[benformatics]

IDR is ideal for narrow peaks.

You can run it on broad peaks but it doesn't seem to be advisable (overly conservative):

• https://github.com/ENCODE-DCC/chip-seq-pipeline2/issues/30
• https://groups.google.com/g/idr-discuss/c/_a_GKfw7kwM?pli=1