How to make the average Hi-C profiles for hg38

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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How to make the average Hi-C profiles for hg38 #67

Closed koh2ng0 closed 11 months ago

koh2ng0 commented 2 years ago

Hi, I tried to make the average Hi-C profile for hg38. So, I downloaded the hic files of 10 cell types for hg38 and created "KRobserved.gz" and "KRnorm.gz", respectively. Then I ran the 'makeAverageHic.py' and got the "avg.gz". But the 'predict.py' requires two Hi-C files, "~.KRobserved.gz" and "~.KRnorm.gz". I don't know what I can do for the next step, so could I get advice for this situation, please?

zzhoujialu commented 1 year ago

Hi, I have met the same problem. Have you solved that yet? Looking forward to hearing from you! :)

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

we mention how to use average Hi-C in the detailed methods of ReadTheDocs