Seeking simple HiC mapping and visualization tutorial for small genome

Question

[rsharris]

I have Arima HiC reads and a 600Mbp assembly.

I've been looking for a bare-bones get-me-started tutorial that can tell me how to map the reads to the assembly, produce the contact information in the right format, and then set it up for visualization.

From what I've read, HiGlass is the best visualization tool, and Juicebox is also widely used.

I have no prior experience using HiC, other than using a HiGlass server set up by another lab to visualize their own data.

Thanks for any help,
Bob Harris

[alex.zaccaron]

I think there are quite a few different workflows to produce a HiC heat map out there. In the past, I was successful in getting a .hic file and load into Juicebox using the scripts provided by PhaseGenomics from here. But it's difficult to run for the first time. More recently, I was able to get a heat map with HiCExplorer. It's better document and easier to use. They provide an example workflow here that you can follow.

[rsharris]

Thanks Alex. (I would have replied earlier, but my biostars acct apparently doesn't notify me when there are responses to my posts).