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macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
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call summit q-value in bigwig file #451

Open sklasfeld opened 3 years ago

sklasfeld commented 3 years ago

To call peaks from multiple replicates I first extended the reads, normalized the signal in each replicate, and then took the average signal at each base pair using my own code. I then did the same for the multiple replicates of the control I have. I then compared the ChIP to the control bigwigs using bdgcmp -m qpois. Then I used the output of this command for input to bdgpeakcall which gives me a narrowPeak file of significant regions and their region q-values. However, I would like to obtain the summit q-values. Is this possible?

taoliu commented 3 years ago

Thanks for asking! If you want to get the 'summit' q-value which is the maximum q-value within the peak, you can check the fifth column of the output narrowPeak file then divide it by 10.