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broadinstitute / ABC-Enhancer-Gene-Prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
MIT License
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EnhancerList.txt can be used as a normal enhancer list? #153

Closed wbszhu closed 6 months ago

wbszhu commented 10 months ago

Hi,

I used ABC model indentifiy the Candidate enhancer regions and i found that some region locate in promoter region. like this

chr13   190285380       190287621       chr13   190285380       190287621       promoter|chr13:190285380-190287621
chr13   191661966       191663614       chr13   191661966       191663614       intergenic|chr13:191661966-191663614
chr13   192248968       192250135       chr13   192248968       192250135       promoter|chr13:192248968-192250135
chr13   192252589       192253327       chr13   192252589       192253327       genic|chr13:192252589-192253327
chr13   192357827       192359219       chr13   192357827       192359219       promoter|chr13:192357827-192359219
chr13   192373107       192374412       chr13   192373107       192374412       promoter|chr13:192373107-192374412
chr13   192376187       192377427       chr13   192376187       192377427       promoter|chr13:192376187-192377427
chr13   192422661       192424370       chr13   192422661       192424370       promoter|chr13:192422661-192424370
chr13   192536847       192537347       chr13   192536847       192537347       intergenic|chr13:192536847-192537347
chr13   192538515       192539367       chr13   192538515       192539367       intergenic|chr13:192538515-192539367

But as usual, we think that enhancer not overlap with promoter.

Thanks in advance

Lu Zhang

atancoder commented 6 months ago

This is intended. See https://abc-enhancer-gene-prediction.readthedocs.io/en/latest/usage/methods.html#defining-and-adding-gene-promoters