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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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Creating .hic from bedpe using Pre #270

Closed cgirardot closed 2 years ago

cgirardot commented 2 years ago

Dear, This is a question regarding the creation of .hic files from binned data.

I used to create .hic from bedpe file eg 

chr2L   5000    10000   chr2L   5000    10000   26
chr2L   5000    10000   chr2L   10000   15000   1
chr2L   5000    10000   chr2L   30000   35000   1
chr2L   5000    10000   chr2L   40000   45000   1
chr2L   5000    10000   chr2L   60000   65000   3
chr2L   5000    10000   chr2L   70000   75000   1

but I cant see bedpe being supported anymore https://github.com/aidenlab/juicer/wiki/Pre#file-format. I am still using juicer_tools_1.11.09_jcuda.0.8.jar for this and it seems to work.

Have you dropped support for bedpe in recent releases?

Thx

sa501428 commented 2 years ago

Bedpe was never a supported format for making .hic files. You'll want to convert to one of the accepted formats. We use the bedpe format for saving loops, domains, etc.

cgirardot commented 2 years ago

ohhhh I am sorry, my bad. I indeed convert the bedpe on the fly to "Short with score format". Sorry for wasting your time and thank you for being my rubber duck!

sa501428 commented 2 years ago

No worries! :)