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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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Can I generate an asymmetric .hic file for an asymmetric matrix, and to illustrate the unsymmetric matrix by JuiceBox? #319

Closed luoxun-xl closed 1 year ago

luoxun-xl commented 1 year ago

Hi, RNA-DNA interaction pairs data could produce an asymmetric contact matrix. So could I generate an unsymmetric .hic file for an asymmetric matrix, and visualize the asymmetric matrix by JuiceBox?

sa501428 commented 1 year ago

Yes, you'd have to make it an inter-chromosomal region. For example, chr1 would become instead be 2 pseudo chromosomes, dna_chr1 and rna_chr1. You can then view this in juicebox under the inter-chromosomal contacts. If you want to load 1d tracks, they would have to be similarly named (dna_chr1, rna_chr1, etc).

luoxun-xl commented 1 year ago

Hi, I tried what you said, and it did work.

However, it is a little bit of a flaw in that there are two-part images like the following. Is there any way to fix this?

image

sa501428 commented 1 year ago

Can you clarify what the issue is? The all-by-all map is usually just for navigation. Once you click on a specific inter-chromosomal region, you should be able to explore it without issue?

If the goal is to specifically plot the all-by-all map, you may want to use straw instead.