Hi-C track: normalization and resolution

[ianakim]

Hi, is it possible to change the applied normalization vector in the HicTrack config from KR to any other? Also, how can I set the default resolution at which to show the hiC data by default?

Thank you and best wishes,
Iana

[cmdcolin]

thanks for posting this. I think that neither of these is immediately possible. I will go ahead and re-open the issue you posted and it can be a feature request tracked from there :)

[ianakim]

thanks a lot, Colin!

[cmdcolin]

I made a proposal for this in #4628

example screenshot

if you want to try out this branch and use jbrowse-web, you can use

jbrowse create --branch normalization_schemes_hic newinstance

this will get that PR beta branch. it has the ability to adjust the default resolution through what I refer to as a 'default multiplier' to the resolution. if instead you want to pick a precise bin size, that could maybe be done too, but the concept of resolution as just a sort of arbitrary multiplier has been in place for a little while now

so you could say, resolutionMultiplier of 10 (basically makes it think it is zoomed out by a factor of 10) on the adapter and it will show bigger squares by default. let me know if that seems ok

{
      "type": "HicTrack",
      "trackId": "hic",
      "name": "Hic Track",
      "assemblyNames": ["hg19"],
      "adapter": {
        "type": "HicAdapter",
        "resolutionMultiplier": 10,
        "hicLocation": {
          "uri": "https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic",
          "locationType": "UriLocation"
        }
      }
    }

note a similar thing was done for bigwig also with resolution #4619

[cmdcolin]

(note that I didn't add configuring normalization type yet but I could add that too potentially)

[cmdcolin]

released in v2.16.1, if you have a chance to try it out let me know