Problem visualizing output (.hic files) in UCSC

[Helen]

Hi, 

I have generated some .hic files in juicer and have uploaded them to UCSC via their track hub. However, I am running into problems with this. I believe the problem is that UCSC is expecting chromosomes to be labelled chr1, chr2 etc. but in my data they are labeled 1, 2 etc. Is there a way to alter this easily in the .hic file without having to change the nodups file and rerunning pre? 

Best wishes, 

Helen 

[Jonathan Casper]

Hi Helen,

I work at UCSC on the Genome Browser.  We should have support in place for the way Juicer sometimes adapts chromosome names; I'm sorry to hear it's not working for you!  Are you be able to give me a bit more information?  A saved UCSC session would be great, but a link to your hub and the name of the assembly you're working on would also help a lot.  If you don't want to post that information in public, you can also email me privately or contact our private mailing list at genom...@soe.ucsc.edu.

Thanks,

Jonathan Casper

UCSC Genome Browser

[Mark Mackiewicz]

I have run into the same problem as Helen, is there a workaround solution for this?

Thanks,

Mark