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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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hicCompareMatrices without normalization #677

Closed yxsee closed 3 years ago

yxsee commented 3 years ago

I have 2 matrices which are normalized by cell count instead of read count, in an attempt to view global increases or decreases in chromatin contacts. I would like to compare the matrices using hicCompareMatrices but I think the matrices are normalized by read count automatically before the log2ratio is performed. Is it possible to run hicCompareMatrices without the normalization step? Thanks!

lldelisle commented 3 years ago

Hi, For the moment, it is not possible. I am working on it #645 ...