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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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bdgdiff output peak numbers don't match up with the narrowPeak results numbers #222

Open ghost opened 6 years ago

ghost commented 6 years ago

Hi Tao Liu,

I'm a researcher in Korea, republic of, using MACS2 for analysing ChIP-seq peaks. I wanted to know how the peaks are different or common in my experiment conditions. (ex. overlaps of cond1 vs cond2, peaks in just cond1, peaks in just cond2) So I followed your instructions you wrote. https://github.com/taoliu/MACS/wiki/Call-differential-binding-events (What's the option -g and -l in the bdgdiff command?? I assumed they are the half point of the extsize and the extsize each. Are they right?)

And I got the result. The result file ".narrowPeak" gave me like 5000 peaks in cond1 and 1000 peaks in cond2. But the result of differential binding command above, gave me that more enriched peaks in cond1 is like 2000 peaks, more enriched peaks in cond2 is 2, peaks enriched commonly are like 600 peaks. Q1. I'm curious where are the rest of the peaks I got from the narrowPeak files?? Q2. Is there any advise you can give me how to get the overlaping peaks and not overlaping peaks in each results using outputs of MACS2??

It'll be very grateful if you could give me some advise or directions.

It's the first time using this git issue section, so if there's anything wrong about the way I wrote 'issue' or said something that are not appropriate, please let me know.

Thank you very much.

Best, Woongjae

Zhenhuiz commented 6 years ago

Hi Woongjae,

Did you find a solution of this problem? I think the problem may come from -C (logLR cutoff. DEFAULT: 3 (likelihood ratio=1000)), but I don't know what it means for common peaks. Peak number of common peaks looks much fewer than from callpeak.

Thank you!