[Gmod-ajax] How to change "genes" trackLabel display feature to Wormbase style

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[Gmod-ajax] How to change "genes" trackLabel display feature to Wormbase style

Keren Zhou
Dear JBrowse team,
      I saw the "genes" trackLabel display feature in WormBase is very cool, just like below:
   I try to configure my browser, but I failed to get the default style just like below:
   Do you know how to configure my file or what extra steps should I take?
    WormBase link(http://www.wormbase.org/tools/genome/jbrowse/?data=data%2Fc_elegans_PRJNA13758&loc=III%3A9040106..9054072&tracks=Classical_alleles%2CPolymorphisms%2CCurated_Genes&highlight=).


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Re: How to change "genes" trackLabel display feature to Wormbase style

Scott Cain
Hi Keren,

I'm guessing the pieces you're missing are the subfeatures (exons or CDSes), right? Or is this a configuration issue?  Please send a sample of the GFF you're using for the gene (basically, one gene's worth of GFF, with all of the subfeatures).  If it's a configuration issue, you can take a look at what I did here: 


where the functions in the curly braces are defined here:


(as an aside, one of the things I really like about JBrowse is that the configurations that people use are "discoverable" in this way)

Scott


On Sat, May 14, 2016 at 1:17 AM, Keren Zhou <[hidden email]> wrote:
Dear JBrowse team,
      I saw the "genes" trackLabel display feature in WormBase is very cool, just like below:
   I try to configure my browser, but I failed to get the default style just like below:
   Do you know how to configure my file or what extra steps should I take?


------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
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Re: How to change "genes" trackLabel display feature to Wormbase style

Colin
Here is a relevant JBrowse FAQ that might apply

http://gmod.org/wiki/JBrowse_FAQ#My_CanvasFeatures_don.27t_show_up_with_subfeatures.2C_why_not.3F

Presumably since this is a Ensembl GFF, the fact that it uses "transcript" as the type instead of "mRNA" commonly means that you have to add this to your track config

    "transcriptType": "transcript"




-Colin

On Tue, May 17, 2016 at 10:44 AM, Scott Cain <[hidden email]> wrote:
Hi Keren,

I'm guessing the pieces you're missing are the subfeatures (exons or CDSes), right? Or is this a configuration issue?  Please send a sample of the GFF you're using for the gene (basically, one gene's worth of GFF, with all of the subfeatures).  If it's a configuration issue, you can take a look at what I did here: 


where the functions in the curly braces are defined here:


(as an aside, one of the things I really like about JBrowse is that the configurations that people use are "discoverable" in this way)

Scott


On Sat, May 14, 2016 at 1:17 AM, Keren Zhou <[hidden email]> wrote:
Dear JBrowse team,
      I saw the "genes" trackLabel display feature in WormBase is very cool, just like below:
   I try to configure my browser, but I failed to get the default style just like below:
   Do you know how to configure my file or what extra steps should I take?


------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
[hidden email]
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
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