BR: Overlapping peaks in the output

[angelosarmen]

Describe the bug Some peaks in *.gappedPeak overlap.

To Reproduce The following two peaks overlap in example output 65283_chr22_peaks.gappedPeak:

chr22	37484220	37485340
chr22	37485300	37487330

Expected behavior I would expect called peaks not to overlap.

Is this because HMMRATAC joins central regions with adjacent nucleosome regions and therefore two central regions separated by a chromosome region are reported as separate peaks? If so, it would be sufficient to post-process the output with bedtools merge. Nevertheless, I think that the possibility of overlapping peaks should be clearly stated in the guide and help.

[angelosarmen]

Hi,

May I kindly remind you to take a look at this.

Thank you.