Is it possible to include HiC data for GRCh38?

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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Is it possible to include HiC data for GRCh38? #64

Closed gaoyuanwang1976 closed 11 months ago

gaoyuanwang1976 commented 2 years ago

Hi dear developers of the ABC model, I'm using ABC model for data of build GRCh38. Up to now, I was only able to run predict.py without using HiC data and only with power law estimate. For a quantitative comparison with other results, I would like to also run predict.py with HiC data. However, juicebox_dump.py seems to be unable to process GRCh38 HiC. Is there a way to workaround for using GRCh38? Do you have an average HiC for GRCh38? Thank you

koh2ng0 commented 2 years ago

@gaoyuanwang1976 Hi, Did you find any solutions for your question?

atancoder commented 11 months ago

We've revamped the codebase. Please check out https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/main and reopen your issue if it still exists

average HiC is available in the linked ReadTheDocs in the detailed methods section