When we prepare the sampleSheet matrix for the DiffBind::dba function, we may have 2 columns for bam files - 1 for ChIP bam and 1 for Input/IgG bam.
Here I have 2 bam files for ChIP and 2 bam files for IgG per sample, and I supply all to MACS2 callpeak (two bams after the -t and two bams after -c),
This would output 1 single output narrowPeak per sample.
In such case how to write the sampleSheet matrix? Do you think I should put the 2 ChIP(or IgG) bams into two different rows on the same column?
My 2 bam files for ChIP(IgG) are actually from 2 replicates. My purpose of doing things above is to merge replicates - which of course can be done in other ways.