Muhammad Saad Shamim

Recently came across this tool while exploring different model visualizations. I really like the look of the examples, but it would be amazing to just plug in a keras model...

How does HiCExplorer handle/read `.hic` files? Easiest option would be to use the latest version of [straw](https://github.com/aidenlab/straw/tree/master/pybind11_python). Alternatively, details about the new format are in [this repo](https://github.com/aidenlab/hic-format).

Was this a forwarded message?

Apologies for the delay. Just answered on the forum. Changing the scope of this report for Github Issues.

Also see this thread https://github.com/aidenlab/juicer/issues/207

`Exception in thread "main" java.lang.RuntimeException: Unknown command: statistics at juicebox.tools.HiCTools.main(HiCTools.java:98)` Is due to using an old Juicer Tools jar that is not compatible with Juicer 2. You'll need to grab...

If it's requesting the `statistics` command, try using a new Juicer Tools jar, e.g. https://github.com/aidenlab/Juicebox/releases/tag/v.2.13.07 Did you clone the github repo for Juicer, or download the 1.6 release?

You'll see a juicer_tools.jar listed under the assets for that release (even though it's in the Juicebox github repo). This is mentioned here: https://github.com/aidenlab/juicer/wiki/Download#version-2xxxx If you cloned the repo, you...

@Aannaw can you make a separate github issue post and include more details about the exact error you are getting?

You are likely falling into this issue. https://github.com/aidenlab/juicer/wiki/FAQs#juicer-pre-is-taking-a-very-long-time https://groups.google.com/g/3d-genomics/c/cE9DPdPGzdY/m/ZfvE9Dd9AAAJ