Quick Q regarding MACS2. The manual states that the
--scale-to option serves to "scale the larger sample up to the smaller sample" or vice-versa. What exactly does it mean by this? Is this scaling only applied when multiple samples/reps are given? Or does it also apply to a sample / control pair?
Context: I currently have an ATAC-seq dataset with a control BAM that has ~ 1/4 as many reads as the sample BAMs - can MACS2 work with this? I've been getting many more peaks without the control than with it.
Thanks in advance for any help! Max