Regarding Diffbind, How does diffbind calculate common peaks with the samples. I'm observing that certain peaks identified as common using bedtools intersect are not appearing in the output report file generated after DiffBind analysis
Command used to write the file : res_deseq <- dba.report(dbObj_analyze,th=1, method=DBA_EDGER,bCalled=TRUE)
Any comment or suggestion would be highly appreciated, either about my approach with DiffBind or recommending other tools.
Thanks in advance!