Hi,

In the current version of DiffBind what are the steps for indicating that PE data is being used? Thank you.

Rob

Hi,

DiffBind doesn't account for PE data.  (Yes, it should, but it doesn't.)  Either just use forward-strand reads, or make sure that all your data are PE, then it'll just count each end independently.

Cheers,

 - Gord

Updating this to reflect that DiffBind has supported PE data for a couple of years now.

The most recent version will automatically detect SE or PE from the bams and perform the counting appropriately.