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LiuLabUB / HMMRATAC

HMMRATAC peak caller for ATAC-seq data
GNU General Public License v3.0
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BR: Overlapping peaks in the output #75

Open angelosarmen opened 4 years ago

angelosarmen commented 4 years ago

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 commented 3 years ago

Hi,

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

Thank you.