I am currently trying to call peaks of a ChIP-Seq experiment using MACS2.
Not every ChIP-Seq replicate has its own corresponding input file. I was thinking of using macs2 with multiple treatment-files (tfiles) and control-files( cfiles) (even if the number of tfiles and cfiles are not the same. For example: 3 tfiles, 2 cfiles or 5 tfiles, 1 cfile) like this :
macs2 callpeak -t tfile1.bam tfile2.bam tfile3.bam -c -cfile1.bam cfile2.bam
Does macs handle this difference in file count via some kind of normalization automatically or do I have to change my set-up in a way for macs2 to work properly?
I really appreciate your thoughts on the topic!
Thank you in advance