How to convert matrix generated by HiCExplorer to N x N matrix

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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How to convert matrix generated by HiCExplorer to N x N matrix #523

Closed BenxiaHu closed 4 years ago

BenxiaHu commented 4 years ago

Hi, I have run HiCExplorer to make Hi-C matrix. Now I want to convert that matrix into N x N format. Do you know how to do that? Best,

joachimwolff commented 4 years ago

Hi,

Not quite clear what do you by NxN matrix. It is highly recommended to use either the cool format or the h5 format to process Hi-C data, text files are a really bad choice.

LeilyR commented 4 years ago

Although, we really discourage you to use text formats for HiC matrices, there is a possibility of converting your .h5 or .cool matrix to it using hicConvertFormat (homer, ginteractions) .