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dozmorovlab / HiCcompare

Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices
https://dozmorovlab.github.io/HiCcompare/
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Can it work for inter-chromosome differential interaction? #13

Closed qianXX closed 4 years ago

qianXX commented 4 years ago

Hi!

I ues this software to find differential interactions.My input is HiC-Pro format.

I can get results by following your document. But your document seem to work on single chromosome. Now I want to know, can it work for inter-chromosome differential interaction?

Thanks!

mdozmorov commented 4 years ago

No, HiCcompare doesn't work on inter-chromosomal matrices. They are non-symmetric, so the concept of distance used for the joint normalization and differential analysis is much harder.