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aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
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how to get sparse matrix for all chromosomes using juicer dump #303

Closed jiangshan529 closed 1 year ago

jiangshan529 commented 1 year ago

Hi, It seems that Juicer dump can only get sparse matrix for a certain chromosome at one time. Is there a way to get matrix from all chromosomes? Thanks!

sa501428 commented 1 year ago

I would check out straw; it has some methods that can get a dense matrix (e.g. as a numpy matrix) and is the preferred tool for extracting data from hic files: https://github.com/aidenlab/straw