I run MACS2 by the following command:
/data/Software/MACS2-126.96.36.19931216/build/scripts-2.7/macs2 callpeak -B -t $bam1 -c $bam2 -n $s --nomodel --extsize 180 --SPMR
I want to remove input signal from the treatment. Can I just xxx_treat_pileup.bdg - xxx_control_lambda.bdg to get what I want?
My situation is that I have 2 treatments and 2 controls. I uploaded 2 treatments' bdg files and peak files to the IGV and I found that in a region the first treatment called more peaks than the other. But there were hardly any difference could be found in bdg files. I wondered if there were differences in control files. And it was true. So I want to remove control signal from treatment to get a more clearly bdg files which can reflect the difference between two samples. Can I do this?