[Gmod-ajax] hic track on jb2

[Ying S. <yy...@sa...>]

Hello,

I am a bioinformatician works on the Darwin Tree of life project in Sanger institute (https://www.darwintreeoflife.org/). I am currently investigating jbrowse2 functionality, and think it could potentially replace our dated genome curation platform(gEVAL).  I have a couple of questions/problem would like to have your help.


  1.  I noticed bionano plugin is available, I also noticed the plugin was developed in 2016, would it work in jb2?
  2.  I use jbrowse cli to load the tracks and assembly. Assembly fasta loads fine,  but bed files and hic files are problematic for me. The hic track doesn't show at all. I have changed the scaffold name in the fasta to capitals but still nothing showed. The following is the command I used to load the hic file. The hic can be displayed in juicebox as I have checked.

jbrowse add-track ~/data/bPtePen1_1/bPtePen1_1_arima.hic -l symlink -a bPtePen1_1



and in the json:

"tracks": [

    {

      "type": "HicTrack",

      "trackId": "bPtePen1_1_arima",

      "name": "bPtePen1_1_arima",

      "adapter": {

        "type": "HicAdapter",

        "hicLocation": {

          "uri": "bPtePen1_1_arima.hic",

          "locationType": "UriLocation"

        }

      },

      "assemblyNames": [

        "bPtePen1_1"

      ]



Could you please help





Kind regards

Yumi



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