Question: macs2 output-narrowpeak file understanding?
gravatar for catherine12243
5.4 years ago by
United States
catherine12243140 wrote:

I used MACS2 to call peaks, and one file with NAME_peaks.narrowPeak, 5th column is "integer score for display" according to the documentation. But I don't understand what that means and how did they get the numbers. Also when I put it into IGV, peaks showed in color difference, and each peak may have more than one peaks labelled as peak#a,b,c...The more "subpeaks", the darker the peak color displayed. Is it related to the "integer score for display"? 

Thank you

chip-seq macs • 4.1k views
ADD COMMENTlink modified 4.6 years ago by Ulduz20 • written 5.4 years ago by catherine12243140
gravatar for Ulduz
4.6 years ago by
Ulduz20 wrote:

The 5th column is for UCSC browser display only. So in UCSC, you will see the stronger peaks darker and weaker peaks lighter.

ADD COMMENTlink written 4.6 years ago by Ulduz20
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