Re: [Gmod-ajax] hic track on jb2 [EXT]

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

With the BED file, it is likely a similar thing: JBrowse expects the names
to exactly match, even the capitalization. You can standardize this or
alternatively configure refNameAliases. refNameAliases allows different
names to be interpreted as coming from the same source

See
https://jbrowse.org/jb2/docs/config_guide/#configuring-reference-name-aliasing
for example

-Colin

On Fri, May 20, 2022 at 9:59 AM Ying Sims <yy...@sa...> wrote:

> Hi Colin,
>
>
>
> Thanks for getting back to me.
>
>
>
> I am sorry the content has repeatedly shown in differently places, I
> wasn’t sure where to get immediate help. As addressed in the previous
> email, JB2 would highly likely used as gEVAL replace, it would become an
> essential tools in Darwin tree of life, I am eagerly making it fully
> functionable.
>
>
>
> It would be great that bionano plugin is available soon, it would make
> huge convenience to our genome evaluation work. Please let me know anything
> we could do at our ends.
>
>
>
> I have another question regarding bed file track. Similar issue as it
> doesn’t show on the browser. The bed file is in gz together with tbi, the
> content is as below:
>
> scaffold_1           233421 233621
>
> scaffold_1           275958 276158
>
> scaffold_1           891914 892114
>
> scaffold_1           3507111               3507311
>
> scaffold_1           5410752               5410952
>
>
>
> I wonder if the name of scaffold has to be capitals?
>
>
>
>
>
> Kindest
>
> Yumi
>
>
>
> *From: *Colin <col...@gm...>
> *Date: *Thursday, 19 May 2022 at 19:31
> *To: *Ying Sims <yy...@sa...>
> *Cc: *"gmo...@li..." <gmo...@li...>
> *Subject: *Re: [Gmod-ajax] hic track on jb2 [EXT]
>
>
>
> 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
> [github.com]
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_jbrowse-2Dcomponents_issues_2962&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=X9VPYUGy4ibZarh9Rup1XaZ62i2u-I0xOZXEy11dXDM&m=2h4i5rjVAcMUOLuJG5ET8RL8r1px37m0nkj5yAy1VdKoa8DBqDWo4DqgwkuPfpJp&s=VE2KzZVtvhWMDUrKzKZ4pJZpopf4Gt2dThdSQ5fbUgw&e=>
> :)
>
> 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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> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dajax&d=DwMFaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=X9VPYUGy4ibZarh9Rup1XaZ62i2u-I0xOZXEy11dXDM&m=2h4i5rjVAcMUOLuJG5ET8RL8r1px37m0nkj5yAy1VdKoa8DBqDWo4DqgwkuPfpJp&s=_T5ACLam-8aQRKMlkktsC7WaVci2zsSyX_BZVxiwRbo&e=>
>
> -- 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.
>