Q: scale-to and downsample options with only treatment files?

[jfreimer]

I am trying to generate a set of consensus peaks from a number of ATAC-Seq samples. A number of papers pool all of the samples and call peaks on the pool. It looks like I can just input all of the samples at once in MACS2 using -t sample1 sample2 sample3.... However, I want to make sure that all of the samples equally contribute to peak calling and some samples don't dominate others just because they have more reads.

I was unclear if the --scale-to or --down-sample commands will scale all of the samples equally within treatment or if they only scale treatment vs. control?

Thank you