Hi everyone!

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.

Thank you!

If you essentially combined multiple BAM files in the MACS call, you could then just combine them using samtools cat, in which case you only need one row per sample.