Convert Galaxy output HiC file to .hic file for use on UCSC Genome Browser

I have been working through the HiCExplorer hands on tutorial in anticipation of developing a file that could be used on the UCSC genome browser. (I was given to understand that this would be possible.) However, if I understand correctly, the end file from HiC Explorer will be .h5. I can’t find any tool to convert a file from .h5 to .hic, which is the format useable on the UCSC Browser. Hoping for some clarification. Thanks!

Hi @acta1

I haven’t done this before, so let’s start at the beginning and figure it out. We can pool in more help as needed.

As a baseline, I just started up a fresh run of the Hands-on: Hi-C analysis of Drosophila melanogaster cells using HiCExplorer / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer / Epigenetics tutorial in this shared history https://usegalaxy.eu/u/jenj/h/galaxy-workflow-galaxy-hi-c-1.

That will take some time to process :slight_smile:

Hi, Jennifer,
Thank you for your response. I have now found tools to convert from cool to hic, and from h5 to cool. I am going to see how far I get with that. I plan to try it with the .h5 file that I got as an endpoint in the tutorial. This may take me a while, but I will get back to you.