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Confused by MACS2 --scale-to option

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

macs2 macs chip atac
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written by maxrwjones • maxrwjones

1 answer

It happens when you have -t and -c, then the counts are downscaled to the smaller of the two.

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written by ATpoint ATpoint

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?

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written by maxrwjones • maxrwjones

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