Question: Can I calculate histonmodification density by xxx_treat_pileup.bdg - xxx_control_lambda.bdg?
gravatar for liuxiaomeng90
5.7 years ago by
liuxiaomeng9070 wrote:

I run MACS2 by the following command:

/data/Software/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?

Thank you!

macs2 • 1.3k views
ADD COMMENTlink modified 5.5 years ago by Biostar ♦♦ 20 • written 5.7 years ago by liuxiaomeng9070
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