Can I input peak files from Genrich as input reads in DiffBind?
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@gsenevirathne-20261
Last seen 5.0 years ago

Hi,

I have been running Genrich (similar to MACS2) as way of calling peaks for my ATAC-seq analysis. My output files from the Genrich are .log and .narroPeak files. Can I use the peak files in DiffBind?

Thanks!

Gayani

DiffBind Genrich • 2.0k views
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Rory Stark ★ 5.1k
@rory-stark-5741
Last seen 9 weeks ago
Cambridge, UK

Yes, this should work with the .narrowPeak files. In the sample sheet, the values in the PeakCaller column should be set to "narrow".

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Thank you for the quick response! It worked.

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In genrich you can input all the replicates for a group and get one .narrowPeak file. Is it ok for the DiffBind sampleSheet to have the same .narrowPeak file for multiple replicates? Or do we need to generate a unique peak file for each sample/replicate?

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Yes, you can use the same peak file for multiple samples!

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