Confused by MACS2 --scale-to option
1
0
Entering edit mode
7 weeks ago

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 • 181 views
ADD COMMENT
2
Entering edit mode
7 weeks ago
ATpoint 55k

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

ADD COMMENT
0
Entering edit mode

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?

ADD REPLY

Login before adding your answer.

Traffic: 1620 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6