macs2 output-narrowpeak file understanding?

Question

[catherine]

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

Answer 1

[Ulduz]

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