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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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KRnorm #19

Closed BenxiaHu closed 3 years ago

BenxiaHu commented 3 years ago

Hi, I am trying to use HiCcompare to jointly normalize multiple Hi-C. After running hic_loess, do I need to run KRnorm to normalize individual normalized matrix made by hic_loess?

mdozmorov commented 3 years ago

No. HiCcompare normalized both matrices to minimize differences between them. Note that HiCcompare normalizes two matrices, but KR is for individual matrices.