What is the best way to calculate the distance of diferent locus on Genome based on the Hi-C data?

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Ilya M. Flyamer

You mean physical distance? That's very non-trivial, and you can't really, because Hi-C reveals a population-average, and in single cells distances vary greatly between them. You could try to calibrate your Hi-C by FISH in your cells, and then roughly estimate other distances. There was a paper/programme about it, but I don't remember the name...

The most comprehensive is the main dataset from Rao et al 2014.

Iman (Abdollah) Dehzangi

Thanks Ilya,

You could not answer my question any better. Thanks and really appreciate it.