How is "integer score for display" calculated in MACS2
Entering edit mode
5.1 years ago
Vanilla ▴ 110

Hi all,

In the MACS2 output file "NAME_peaks.narrowPeak", there's a column called "integer score for display". I found the score is not proportional to the 7th column "fold-change".

For example, I have two peaks. The "integer score for display" and "fold-change" for these two are:

peak1 207 3.21293

peak2 268 3.16602

So for peak1, the "fold-change" is higher than peak2, however, its "integer score for display" is lower than peak2.

And the "integer score for display" is also not proportional to "pileup height at peak summit" (6th column in "NAME_peaks.xls").

As I didn't find any description about this score in their papers, I'm wondering how the score is calculate? How could I understand this "integer score for display" properly? I mean how this score represent the intensity/affinity of TF binding?

Thanks all!

ChIP-Seq MACS2 narrowPeak • 3.9k views
Entering edit mode
5.1 years ago
igor 12k

This was actually addressed by the MACS developer:

The score is for 'display' purpose only. It's for UCSC browser and will make stronger peaks darker, and weaker peaks lighter.


Entering edit mode

Hi Igor,

Thanks very much for your answer. Actually their explanation is still vague, and I still didn't get how this score can reflect how strong the peak is.

But anyway, as they suggested using column7-9 for downstream, I may only take this score for visualization but not used for filtering.

Thanks again for your help.


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