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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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"Chr" removed from the .hic file #118

Closed ghuryejay closed 5 years ago

ghuryejay commented 5 years ago

Hi,

I am providing my own chrom_sizes.txt file for juicer pre to dump a .hic file. The chromosome names in my file are like "chr1, chr2, chr3,...". However in the .hic file, the chromosome names are like "1,2,3,...". Is there any way to preserve the original names in the final .hic file? I want to use the original names.

nchernia commented 5 years ago

@sa501428 - not sure this is possible, thoughts?

sa501428 commented 5 years ago

@machinegun in which context do you want the chr preserved? Are you talking about the Juicebox dropdown? Straw? Some other analysis tool?

ghuryejay commented 5 years ago

Arrowhead and Hiccups. If I use it to call domains, the output file has chromosome names as 1,2,3... Also if the chromosome names are something else like 'contig-1', then it caps the name, so the name in arrowhead output file is like 'CONTIG-1'.

sa501428 commented 5 years ago

This points to a broader question that I recall Olga @dudcha also had regarding what standards should be. We implemented these steps to resolve bugs when users were using different capitalizations / varying inclusion of 'chr', but all were trying to use hg19. To resolve that, we remove chr in Juicebox and capitalize everything. This allows users to load annotations/files with different labels (1, chr1, CHR1).

ghuryejay commented 5 years ago

Cool. Thanks!

YichaoOU commented 4 years ago

Hello,

How can we let juice_tools not remove chr and not cap the letters?

Thanks!

sa501428 commented 4 years ago

What version of the jar are you using?

YichaoOU commented 4 years ago

juicer_tools_1.13.01.jar

sa501428 commented 4 years ago

Can you try a newer jar? I recall we removed this restriction for non-human genomes.

YichaoOU commented 4 years ago

ok, will try, I'm using a custom genome, so I gave the program a chrom.size file, not specifying hg19.

YichaoOU commented 4 years ago

Hello,

I tried 1.21.01, still chr is remove and everything is cap.

Is there a programmable way to rename the chr?

YichaoOU commented 4 years ago

I think I have tried all the different versions. I think I can re-compile the jar file if you can tell me which line to change.

jeramiahsmith commented 8 months ago

This still seems to be an issue in recent versions, Is there a fix? It makes it difficult to view Juicer output in nonhuman UCSC browsers.

sa501428 commented 8 months ago

This issue was fixed a while back; you can grab the latest jars here: https://github.com/aidenlab/Juicebox/releases