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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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How to normalize the data for bdgdiff #518

Open liuyu988 opened 2 years ago

liuyu988 commented 2 years ago

Hi,

I would like to detect differential peaks between two different conditions by macs2 bdgdiff and use -d1 depth_condition1 -d2 depth_condition2. But I don't know whether to normalize the data from different chip-seq and how to normalize?

Thanks a lot!

Yu

taoliu commented 2 years ago

You don't need to normalize the data. You can use both of the bedGraph files of the 'raw pileup' (e.g. the pileup function, orcallpeakfunction) from MACS, then provide the sequencing depth for--d1and--d2`. Check: https://github.com/macs3-project/MACS/wiki/Call-differential-binding-events