Hello Dear community,

I am trying to apply DiffBInd package to perform a binding analysis of two TFs from the same family, TF1 and TF2. My goal is to understand to what extend these two TFs act cooperatively so we have ChIP-seq data of both, 2 replicates of each. I have been reading carefully DiffBind's documentation, some other tutorials and posts in forums like this but still very confused of how DiffBind works.

My question is why the output of the differential binding analysis does not include all consensus peaks? in my analysis there are a couple hundred missing

If I would like to obtain peaks bound by both TFs, I guess these missing peaks from the consensus peakset should be included too. Am I correct?

Is doing a differential analysis and retrieving the least changing peaks the best way to obtain the two TFs' common peaks?

Thanks in advance

Alejandro