Re: [Gmod-ajax] hic track on jb2

[Colin <col...@gm...>]

Hi Ying,
I think some of this dialog is continued in various other places
(github/gitter) but to answer


1) JBrowse 1 plugins will not work with JBrowse 2 unfortunately, but as you
have done, a request for support is here
https://github.com/GMOD/jbrowse-components/issues/2962 :)
2) I think you said that this was resolved, now, by making the scaffold
names match the FASTA, but let us know if you have any other concerns


-Colin

On Thu, May 19, 2022 at 9:44 AM Ying Sims <yy...@sa...> wrote:

> 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
> -- The Wellcome Sanger Institute is operated by Genome Research Limited, a
> charity registered in England with number 1021457 and a company registered
> in England with number 2742969, whose registered office is 215 Euston Road,
> London, NW1 2BE.
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