MACS2: What is in 4th column of treat_pvalue.bdg/treat_qvalue.bdg files?

Question

[salamandra]

MACS2 output files, 'treat_pvalue.bdg' and 'treat_qvalue.bdg', contain only significant peaks (with p-value/q-value below user defined threshold).

But is 4th column of these files the difference in intensity (score) between ChIP and Input, or is it intensity (score) for ChIP only?

If it is the intensity for ChIP only, then what tools can get the difference between ChIP and Input intensities?

[1063546746]

hello, I am a freshman in analyzing the ATAC-seq data. I am confused that I can not get 'treat_pvalue.bdg' and 'treat_qvalue.bdg' in the MACS2 output files. Could you like to share your experience with me? Thanks

[salamandra]

For macs2 questions it's better to post at: https://github.com/taoliu/MACS where developers can help you