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SchulzLab / STARE

TF analysis from epigenetic and Hi-C data
MIT License
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Normalization of HI-C matrix #5

Closed Andi964 closed 1 year ago

Andi964 commented 1 year ago

Hello,

Can your method deal with e.g. VC-Normalized contact data or only with KR normalized data? This would be relevant, since sometimes KR does not converge for specific chromosomes if data is sparse.

Best, Andreas

DennisHeck commented 1 year ago

Hello! In theory any normalization should work, as long as the contact frequencies for all candidate enhancers around a gene are comparable. But we didn't test any other method than KR yet for the CRISPRi-validation data. I wouldn't expect it to make much of a difference. Best, Dennis