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JinLabBioinfo / DeepLoop

DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data
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Convert hg19 to hg38 #6

Closed AssumeAssume closed 2 years ago

AssumeAssume commented 2 years ago

Hello, DeepLoop really helps our work. But it gives the results using hg19 coordinates. I wonder if there is anything I can do to convert the cool file from hg19 to hg38 ? Or could DeepLoop gives hg38 results? Thank you

JinLabBioinfo commented 2 years ago

In the HiCorr GitHub page, towards the bottom of the main page, we have an instruction on how to generate reference files for HiCorr. You may follow the example to generate reference files for hg38. This will allow you to analyze hg38.