p value of significance for overlapping peaks

Hi all,

I have MACS2 peaks for two different transcription factors and I want to find the p-value for the significance peak overlapped between these two transcription factors. I can do a hypergeometric test to find the p-value but I do not know how to proceed. Please help me with some example.

Thank you

macs2 chip-seq

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updated 1.9 years ago by i.sudbery

• written 1.9 years ago by qudrat.nii •

1 answer

We use the GAT tool for this. I believe there is an R package that does something similar (shuffles one set of peaks and then compares the overlap after shuffling), although I can't bring its name to mind now.

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written 1.9 years ago by i.sudbery

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