Question: Reading peaks from MACS2 with DiffBind
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gravatar for aviv.de-morgan
5 months ago by
aviv.de-morgan0 wrote:

The peak format required by DiffBind is BED, whereas MACS2 does not output BED files as MACS14 (the earlier release) did. Rather, it outputs BedGraph (bdg) files, or a variant format of a BED file (see here: https://github.com/taoliu/MACS under Output Files), i.e., the *.narrowPeak or *.broadPeak files. How can this be resolved?

ADD COMMENTlink modified 5 months ago by Rory Stark2.9k • written 5 months ago by aviv.de-morgan0
Answer: Reading peaks from MACS2 with DiffBind
0
gravatar for Rory Stark
5 months ago by
Rory Stark2.9k
CRUK, Cambridge, UK
Rory Stark2.9k wrote:

You can read in narrowPeak files by setting the PeakCaller to "narrow" in the sample sheet. Alternatively, you can read in the xls files created by MACS2 by setting the PeakCaller to "macs".

-Rory

ADD COMMENTlink written 5 months ago by Rory Stark2.9k
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