Hello, Recently I'm trying to perform differential binding analysis of ChIP-seq data using DiffBind. I have two group samples, which are from single-end data and paired-end data respectively, and I want to detect differential peaks between the two groups. To do that, firstly I got the dba object by adding all the samples and then run the dba.count() function. However, I found that all FRiP values for single-end data were zero since reads were automatically detected and counted as paired-end (paired-end samples come first in the sampleSheet). Then I reordered the sampleSheet with single-end samples listed first. This time counts were right for S.E but double for P.E, which might affect the outcome.
I also tried to run dba.count() for P.E and S.E groups separately and then combined them using dba.peakset function, but I got error when performed dba.analyze(). So, can DiffBind deal with single-end and paired-end data together? And what should I do if it can? Thank you very much!
Best, Xiaojie Cheng