Reading peaks from MACS2 with DiffBind
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@avivde-morgan-20918
Last seen 2.3 years ago

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?

chip-seq peak calling diffbind • 802 views
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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 2 days ago
CRUK, Cambridge, UK

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

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