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?
Yes, this should work with the .narrowPeak files. In the sample sheet, the values in the PeakCaller column should be set to "narrow".
Thank you for the quick response! It worked.
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?
Yes, you can use the same peak file for multiple samples!
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