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aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
410 stars 181 forks source link

Juicer pre create .hic #188

Closed BenxiaHu closed 2 years ago

BenxiaHu commented 3 years ago

Hi, I also follow this command to run jucer to create a .hic file java -Xmx2g -jar juicebox_tools.jar pre data/test.txt.gz data/test.hic hg19

I want to know what kind of normalization is used by the above-mentioned command.

if not, can I apply ICE to normlize the .hic file generated by _java -Xmx2g -jar juicebox_tools.jar pre_

sa501428 commented 2 years ago

Vanilla Coverage (VC), Square Root of Vanilla Coverage (VC_SQRT), and actual matrix balancing (KR or SCALE). Please use the forum (aidenlab.org/forum.html for general questions)