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  1. IGB
  2. IGBF-3976

Investigate: Visualizing Hi-C data in IGB

    Details

    • Type: Task
    • Status: To-Do (View Workflow)
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
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      Description

      Situation: I talked with Cory Padilla at ASHG 2024 - he's a product manager at Cantata Bio (formerly Dovetail Genomics) which produces Hi-C kits. He is really excited about the idea of collaborating and brainstorming ways in which IGB can visualize Hi-C data and become part of their suggested bioinformatics workflow.

      Task: Reach out to Cory and set up a meeting to discuss ideas for visualizing Hi-C data. We should also look into other genome browsers (specifically Wash-U) and how they currently display Hi-C data. Locating some example data would be a great help, too.

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          pkulzer Paige Kulzer created issue -
          pkulzer Paige Kulzer made changes -
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          pkulzer Paige Kulzer added a comment - - edited

          Unfortunately, Cory's email was not saved correctly via ASHG's app, so I sent him a message on 11/15 via LinkedIn and am waiting to hear back.

          In the meantime, I've looked into Wash-U's documentation and found some instructions for adding HiC data to their browser: https://eg.readthedocs.io/en/latest/dynamic.html#make-dynamic-hic-maps-using-data-hub

          As for data we can use to do this, I suggest using a resource called DNA Zoo. It's a repository of freely available genome assemblies, genome annotations, DNA-Seq data, and Hi-C maps created for non-model species. Here's a link: https://www.dnazoo.org/assemblies

          And here's a bit more information about what each of the HiC files there contain: https://github.com/aidenlab/juicer/wiki/Data

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          pkulzer Paige Kulzer added a comment - - edited Unfortunately, Cory's email was not saved correctly via ASHG's app, so I sent him a message on 11/15 via LinkedIn and am waiting to hear back. In the meantime, I've looked into Wash-U's documentation and found some instructions for adding HiC data to their browser: https://eg.readthedocs.io/en/latest/dynamic.html#make-dynamic-hic-maps-using-data-hub As for data we can use to do this, I suggest using a resource called DNA Zoo. It's a repository of freely available genome assemblies, genome annotations, DNA-Seq data, and Hi-C maps created for non-model species. Here's a link: https://www.dnazoo.org/assemblies And here's a bit more information about what each of the HiC files there contain: https://github.com/aidenlab/juicer/wiki/Data
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            People

            • Assignee:
              pkulzer Paige Kulzer
              Reporter:
              pkulzer Paige Kulzer
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              • Created:
                Updated: