Question: macs2 callpeak results
gravatar for nehoralevi
11 months ago by
nehoralevi0 wrote:


I'm new in bioinformatics in general, and I try to do ChIP-seq analysis.

I used Macs2 for peaks detection for two samples- treatment and control. The command line was identical, but when I looked at the peaks at the UCSC, two problems were revealed:

  1. macs2 recognized the treatment peaks as longer peaks systemically. When there is one long treatment peak, there are few short control peaks, even when it looked the same at the IP and input levels.

  2. many times macs2 found peak only in the treatment even though the IP looked similarly and the input was clean.

Do you know what the problem could be? Or direct me to the right parameters that could be connected to it?

I appreciate the help, Nehora.

chip-seq macs2 callpeak • 548 views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 11 months ago by nehoralevi0

Please upload some screenshots of the regions and describe how these UCSC tracks were generated, especially towards normalization. Also please add all relevant command lines.

ADD REPLYlink modified 11 months ago • written 11 months ago by ATpoint34k

the command line of normalised callpeak was- macs2 callpeak -t $filename3 -c $filename4 -f SAM -g mm -n treatment -B --SPMR -q 0.01 -s 50 --bw 300 --verbose 3 --outdir /home/nehora/Macs2/treatment_normal > treatment.out &

the bed files have been uploaded to the UCSC. I hope I understand your requests. thank you very much!

screenshot of treatment peak only when should be control one as well.

screenshot of shorter peaks in control and one long peak in treatment. the order of the tracks is- peaks, IP, input, the treatment is always above the control

ADD REPLYlink modified 11 months ago • written 11 months ago by nehoralevi0

This sounds like it might be caused by a difference in sequencing depths, either between the treatment and control, or the ratio of the IP and input within each sample.

ADD REPLYlink written 11 months ago by colin.kern900
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