Hi all,

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

Thanks ATpoint! One more quick Q, do you know how this scaling is performed? Is a random subsample of the larger sample taken? Or are all reads used and then the read counts at each bp are scaled by the 'smaller/larger' ratio?