Question: Calling peaks with macs2 if not all replicates have a corresponding input-file
gravatar for jklopp
2.4 years ago by
jklopp0 wrote:

Dear all,

I am currently trying to call peaks of a ChIP-Seq experiment using MACS2.

Not every ChIP-Seq replicate has its own corresponding input file. I was thinking of using macs2 with multiple treatment-files (tfiles) and control-files( cfiles) (even if the number of tfiles and cfiles are not the same. For example: 3 tfiles, 2 cfiles or 5 tfiles, 1 cfile) like this :

macs2 callpeak -t tfile1.bam tfile2.bam tfile3.bam -c -cfile1.bam cfile2.bam

Does macs handle this difference in file count via some kind of normalization automatically or do I have to change my set-up in a way for macs2 to work properly?

I really appreciate your thoughts on the topic!

Thank you in advance

chip-seq macs2 replicates • 1.6k views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.4 years ago by jklopp0

MACS2 will scale the number of reads in your treatment sample down to the number in your control sample. That means you can provide any number/combination of treatment and control samples and MACS2 will scale them accordingly.

ADD REPLYlink written 2.4 years ago by James Ashmore2.7k

Its need not be scaling treatment to control always. It scales the sample with large number of reads to sample with smaller number of reads.

ADD REPLYlink written 2.4 years ago by geek_y9.8k

I would pool all control samples and call peaks on each treatment sample independently.

macs2 callpeak -t tfile1.bam -c ctrl_pooled.bam
ADD REPLYlink written 2.4 years ago by geek_y9.8k

How do u pool all the control sample? can it be done by samtools merge? what will happen if we merge both control and treated samples?

ADD REPLYlink written 20 months ago by me.sr15100

Thank you all for you answers!

ADD REPLYlink written 2.4 years ago by jklopp0
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