Hi, I'm trying to use DiffBind for my ChIPseq analysis, but I encountered the following "problem".
I loaded two patients' groups of samples using dba function and setting minOverlap equal to 2. Same setting also for:
my_peaks <- dba.count(my_peaks, bUseSummarizeOverlaps=F,minOverlap=2).
I defined the contrast and then I ran a differential analysis: my_peaks <- dba.analyze(my_peaks,method=DBA_DESEQ2)
But when I looked into this object: peaks_DF <- dba.report( my_peaks,bCalled=TRUE,th=0.1) I found some peaks present only in 1 one sample for the groupA, and only in one sample for the groupB.
Is there any possibility to avoid this and having only a minOverlap of 2 in each patients' group? I mean at least a minimum of overlap=2 in each considered category (>=2 in the groupA and >=2 in the group B, not >=2 groupA+groupB) to create a consensus on which perform differential analysis.
Thank you in advance for your help!