Hi!
I'm calling peaks and later comparing conditions for a Cut&Run dataset and would like to know what is the recommended approach on using DiffBind.
I have a Control, Treatment (both in triplicates) and relevant IgG for both the conditions. Here in lies my need for a recommendation:
I'm calling peaks with macs. Should I use the IgG for the relevant condition here while calling the peaks, and then provide it the sample sheet under "bamControl" to build greylists?
Skip the IgG during Peak calling, but provide the IgGs as "bamControl"
Use the IgG during Peak calling, and not provide it during DiffBind since the regions identified by the IgG bams would already be relatively free of the non-specific binding events and be somewhat sharp.
Apologies if it already has been asked, and I'd be happy to get pointed in the relevant direction!
Regards, Harish
