macs2 output-narrowpeak file understanding? · Biostar

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macs2 output-narrowpeak file understanding?

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

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updated 4.1 years ago by Ram

• written 11.3 years ago by catherine

1 answer

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

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written 10.4 years ago by Ulduz •

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