gmod-ajax — JBrowse list

Re: [Gmod-ajax] How to add more fields to faceted selector

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

It is now fixed on the main branch (jbrowse create --nightly) if you want
to try it

Fix here https://github.com/GMOD/jbrowse-components/pull/5492

-Colin

On Thu, Feb 26, 2026 at 4:33 PM Vaneet Lotay <van...@uc...>
wrote:

> Hey Colin,
>
>
>
> Thank so much for adding that update so quickly into a new release.  The
> searching of additional metadata fields does work very well but there’s a
> new issue I noticed.  It appears now that if I have any HTML in those
> metadata fields which for my purposes was used for sorting as well as
> adding links to the ‘About this track’ window, the HTML is not escaped now
> in the faceted track selector window and just shows as the raw HTML with
> all the opening and ending tags.
>
>
>
> I can’t quite remember now but I’m pretty sure this wasn’t happening
> before in a previous release.  I remember looking at the metadata in the
> faceted track selector in previous releases and it was escaped so that the
> text appeared as a link when I had put in the necessary HTML to do that.
> The about this track window still appears correctly as before with escaping
> the necessary HTML so it’s not seen.
>
>
>
> Is this something you can fix?
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* February 21, 2026 12:04 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmod-ajax <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] How to add more fields to faceted selector
>
>
>
> [△EXTERNAL]
>
>
>
> Searching metadata in the faceted selector was fixed and released in
> v4.1.13. Let me know if you run into any other issues
>
>
>
> On Thu, Feb 5, 2026 at 10:43 AM Colin <col...@gm...> wrote:
>
> I don't think so. I'll made a tracking issue for this here
> https://github.com/GMOD/jbrowse-components/issues/5472
>
>
>
> On Wed, Feb 4, 2026 at 3:34 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hey Colin,
>
>
>
> Just a follow up to this old topic…thank you for the info by the way!  Is
> there any way to search other fields in the faceted track selector besides
> the track name?
>
>
>
> I realize that when there are metadata attributes that are shared across
> more then 5 tracks those attributes do appear as facets and you can click
> on the facet filters to filter out the results by their values.  However,
> what I’m wondering is there any way to search those additional facets on
> their values from the main search bar of the faceted track selector, or
> does it only simply search the tracknames?
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* October 12, 2025 7:29 AM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmod-ajax <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] How to add more fields to faceted selector
>
>
>
> [△EXTERNAL]
>
>
>
> The basic idea for the faceted track selector is that any "top level"
> entry in the track metadata becomes searchable in the track metadata.
> Example
>
>
>
> {
>       "type": "VariantTrack",
>       "trackId": "volvox_test_vcf",
>       "metadata": {
>         "thing here": "hello"
>       },
>       "name": "volvox 1000genomes vcf",
>       "assemblyNames": ["volvox"],
>       "category": ["Variants"],
>       "adapter": {
>         "type": "VcfTabixAdapter",
>         "uri": "volvox.test.vcf.gz"
>       }
>     },
>
>
>
> That will make "thing here" a column and a facet filter, but also note
> that it filters out "sparse" metadata columns by default, so it only shows
> metadata that is shared across >5 tracks as a facet (arbitrary threshold)
>
>
>
> You can toggle "Show sparse metadata columns" to show facets for even
> metadata not shared by 5 tracks
>
>
>
>
>
>
>
> There is no notion of only a subset of tracks appearing in the faceted
> selector currently
>
>
>
> -Colin
>
>
>
> On Wed, Oct 8, 2025 at 5:16 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hi,
>
>
>
> There is documentation for adding the field ‘category’ as an active field
> to the faceted track selector.  How do you add more fields to that so they
> can be used to filter tracks for in that pop up window?  I tried added some
> random fields under the ‘metadata{}’ name in the config.json file.  While
> they appear in the ‘About this track’ dialog they don’t appear in the
> faceted track selector.
>
>
>
> Also, is there a way I can limit which tracks I want to appear in the
> faceted track selector?  I want a subset of tracks that can appear in their
> own faceted track selector with many metadata fields to filter upon similar
> to the original JBrowse.  How do I do this in JBrowse 2?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Re: [Gmod-ajax] Rewrite the names of 'feature detail' fields in JBrowse2 details

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

Note also that the entire thing is a jexl expression, so alternatively, you
can make a javascript function that jexl can invoke to process the feature
too

Here is an example that is equivalent to the above, using a javascript
plugin that adds a custom jexl callback

// in your plugin, make a new callback. just called formatMyFeature to show
it can be named whatever you want
      pluginManager.jexl.addFunction('formatMyFeature', feature => {
        const ret = {}
        if (feature.gc_content !== undefined) {
          ret.gc_content = undefined
          ret['GC Content'] = feature.gc_content
        }
        return ret
      })

// in your config, invoke the custom jexl function
"feature": "jexl:formatMyFeature(feature)",


On Tue, Mar 3, 2026 at 10:15 AM Colin <col...@gm...> wrote:

> Yes, renaming a field name in the feature details is the process of
> setting the thing you want to rename to undefined and then using the value
> in a new name
>
> Example: if there was a field in gff3 column 9 that said "gc_content" you
> can do something like this
>
>  "feature": "jexl:{gc_content:undefined,'GC Content':feature.gc_content}",
>
>
> On Mon, Mar 2, 2026 at 1:17 PM Vaneet Lotay <van...@uc...>
> wrote:
>
>> Hello,
>>
>>
>>
>> I looked into the documentation for what I’m discussing here and came
>> across this page:
>>
>>
>>
>> https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/
>>
>>
>>
>> From this page I gather, you can add new custom fields to the feature
>> detail panel, and you can remove elements from the feature detail panel by
>> setting them undefined.  However, is there a way I can rename some feature
>> detail elements by changing the names they’re given in the GFF3 file.  I
>> have a bunch of attributes I’ve added to the 9th column in my gff3 file
>> that provide some useful statistics to the tracks.  Because I needed to
>> follow the GFF3 format I had to not include spaces in their names and
>> letter capitalizations would not be pushed forward by default to the
>> panel.  Can I rename these attributes somehow in the config.json file to
>> have different field names while keeping their values the same?  Or is the
>> only solution to set all of them to ‘undefined’ and then create new fields
>> with their values inside them?  If that’s the solution I would prefer to
>> see an example doing this as that could get confusing for me dealing with
>> all the variables under the feature detail panel.
>>
>>
>>
>> Thanks,
>>
>>
>> Vaneet
>>
>>
>>
>>
>>
>

Re: [Gmod-ajax] Rewrite the names of 'feature detail' fields in JBrowse2 details

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

Yes, renaming a field name in the feature details is the process of setting
the thing you want to rename to undefined and then using the value in a new
name

Example: if there was a field in gff3 column 9 that said "gc_content" you
can do something like this

 "feature": "jexl:{gc_content:undefined,'GC Content':feature.gc_content}",


On Mon, Mar 2, 2026 at 1:17 PM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
>
>
> I looked into the documentation for what I’m discussing here and came
> across this page:
>
>
>
> https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/
>
>
>
> From this page I gather, you can add new custom fields to the feature
> detail panel, and you can remove elements from the feature detail panel by
> setting them undefined.  However, is there a way I can rename some feature
> detail elements by changing the names they’re given in the GFF3 file.  I
> have a bunch of attributes I’ve added to the 9th column in my gff3 file
> that provide some useful statistics to the tracks.  Because I needed to
> follow the GFF3 format I had to not include spaces in their names and
> letter capitalizations would not be pushed forward by default to the
> panel.  Can I rename these attributes somehow in the config.json file to
> have different field names while keeping their values the same?  Or is the
> only solution to set all of them to ‘undefined’ and then create new fields
> with their values inside them?  If that’s the solution I would prefer to
> see an example doing this as that could get confusing for me dealing with
> all the variables under the feature detail panel.
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
>
>

[Gmod-ajax] Rewrite the names of 'feature detail' fields in JBrowse2 details

[Vaneet L. <van...@uc...>]

Hello,

I looked into the documentation for what I'm discussing here and came across this page:

https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/

>From this page I gather, you can add new custom fields to the feature detail panel, and you can remove elements from the feature detail panel by setting them undefined.  However, is there a way I can rename some feature detail elements by changing the names they're given in the GFF3 file.  I have a bunch of attributes I've added to the 9th column in my gff3 file that provide some useful statistics to the tracks.  Because I needed to follow the GFF3 format I had to not include spaces in their names and letter capitalizations would not be pushed forward by default to the panel.  Can I rename these attributes somehow in the config.json file to have different field names while keeping their values the same?  Or is the only solution to set all of them to 'undefined' and then create new fields with their values inside them?  If that's the solution I would prefer to see an example doing this as that could get confusing for me dealing with all the variables under the feature detail panel.

Thanks,

Vaneet

Re: [Gmod-ajax] How to add more fields to faceted selector

[Vaneet L. <van...@uc...>]

Hey Colin,

Thank so much for adding that update so quickly into a new release.  The searching of additional metadata fields does work very well but there’s a new issue I noticed.  It appears now that if I have any HTML in those metadata fields which for my purposes was used for sorting as well as adding links to the ‘About this track’ window, the HTML is not escaped now in the faceted track selector window and just shows as the raw HTML with all the opening and ending tags.

I can’t quite remember now but I’m pretty sure this wasn’t happening before in a previous release.  I remember looking at the metadata in the faceted track selector in previous releases and it was escaped so that the text appeared as a link when I had put in the necessary HTML to do that.  The about this track window still appears correctly as before with escaping the necessary HTML so it’s not seen.

Is this something you can fix?

Thanks,

Vaneet

From: Colin <col...@gm...>
Sent: February 21, 2026 12:04 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: [Gmod-ajax] How to add more fields to faceted selector

[△EXTERNAL]

Searching metadata in the faceted selector was fixed and released in v4.1.13. Let me know if you run into any other issues

On Thu, Feb 5, 2026 at 10:43 AM Colin <col...@gm...<mailto:col...@gm...>> wrote:
I don't think so. I'll made a tracking issue for this here https://github.com/GMOD/jbrowse-components/issues/5472

On Wed, Feb 4, 2026 at 3:34 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Colin,

Just a follow up to this old topic…thank you for the info by the way!  Is there any way to search other fields in the faceted track selector besides the track name?

I realize that when there are metadata attributes that are shared across more then 5 tracks those attributes do appear as facets and you can click on the facet filters to filter out the results by their values.  However, what I’m wondering is there any way to search those additional facets on their values from the main search bar of the faceted track selector, or does it only simply search the tracknames?

Thanks,

Vaneet

From: Colin <col...@gm...<mailto:col...@gm...>>
Sent: October 12, 2025 7:29 AM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmod-ajax <gmo...@li...<mailto:gmo...@li...>>
Subject: Re: [Gmod-ajax] How to add more fields to faceted selector

[△EXTERNAL]

The basic idea for the faceted track selector is that any "top level" entry in the track metadata becomes searchable in the track metadata.  Example

{
      "type": "VariantTrack",
      "trackId": "volvox_test_vcf",
      "metadata": {
        "thing here": "hello"
      },
      "name": "volvox 1000genomes vcf",
      "assemblyNames": ["volvox"],
      "category": ["Variants"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "volvox.test.vcf.gz"
      }
    },

That will make "thing here" a column and a facet filter, but also note that it filters out "sparse" metadata columns by default, so it only shows metadata that is shared across >5 tracks as a facet (arbitrary threshold)

You can toggle "Show sparse metadata columns" to show facets for even metadata not shared by 5 tracks



There is no notion of only a subset of tracks appearing in the faceted selector currently

-Colin

On Wed, Oct 8, 2025 at 5:16 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hi,

There is documentation for adding the field ‘category’ as an active field to the faceted track selector.  How do you add more fields to that so they can be used to filter tracks for in that pop up window?  I tried added some random fields under the ‘metadata{}’ name in the config.json file.  While they appear in the ‘About this track’ dialog they don’t appear in the faceted track selector.

Also, is there a way I can limit which tracks I want to appear in the faceted track selector?  I want a subset of tracks that can appear in their own faceted track selector with many metadata fields to filter upon similar to the original JBrowse.  How do I do this in JBrowse 2?

Thanks,

Vaneet
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] How to add more fields to faceted selector

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

Searching metadata in the faceted selector was fixed and released in
v4.1.13. Let me know if you run into any other issues

On Thu, Feb 5, 2026 at 10:43 AM Colin <col...@gm...> wrote:

> I don't think so. I'll made a tracking issue for this here
> https://github.com/GMOD/jbrowse-components/issues/5472
>
> On Wed, Feb 4, 2026 at 3:34 PM Vaneet Lotay <van...@uc...>
> wrote:
>
>> Hey Colin,
>>
>>
>>
>> Just a follow up to this old topic…thank you for the info by the way!  Is
>> there any way to search other fields in the faceted track selector besides
>> the track name?
>>
>>
>>
>> I realize that when there are metadata attributes that are shared across
>> more then 5 tracks those attributes do appear as facets and you can click
>> on the facet filters to filter out the results by their values.  However,
>> what I’m wondering is there any way to search those additional facets on
>> their values from the main search bar of the faceted track selector, or
>> does it only simply search the tracknames?
>>
>>
>>
>> Thanks,
>>
>>
>> Vaneet
>>
>>
>>
>> *From:* Colin <col...@gm...>
>> *Sent:* October 12, 2025 7:29 AM
>> *To:* Vaneet Lotay <van...@uc...>
>> *Cc:* gmod-ajax <gmo...@li...>
>> *Subject:* Re: [Gmod-ajax] How to add more fields to faceted selector
>>
>>
>>
>> [△EXTERNAL]
>>
>>
>>
>> The basic idea for the faceted track selector is that any "top level"
>> entry in the track metadata becomes searchable in the track metadata.
>> Example
>>
>>
>>
>> {
>>       "type": "VariantTrack",
>>       "trackId": "volvox_test_vcf",
>>       "metadata": {
>>         "thing here": "hello"
>>       },
>>       "name": "volvox 1000genomes vcf",
>>       "assemblyNames": ["volvox"],
>>       "category": ["Variants"],
>>       "adapter": {
>>         "type": "VcfTabixAdapter",
>>         "uri": "volvox.test.vcf.gz"
>>       }
>>     },
>>
>>
>>
>> That will make "thing here" a column and a facet filter, but also note
>> that it filters out "sparse" metadata columns by default, so it only shows
>> metadata that is shared across >5 tracks as a facet (arbitrary threshold)
>>
>>
>>
>> You can toggle "Show sparse metadata columns" to show facets for even
>> metadata not shared by 5 tracks
>>
>>
>>
>>
>>
>>
>>
>> There is no notion of only a subset of tracks appearing in the faceted
>> selector currently
>>
>>
>>
>> -Colin
>>
>>
>>
>> On Wed, Oct 8, 2025 at 5:16 PM Vaneet Lotay <van...@uc...>
>> wrote:
>>
>> Hi,
>>
>>
>>
>> There is documentation for adding the field ‘category’ as an active field
>> to the faceted track selector.  How do you add more fields to that so they
>> can be used to filter tracks for in that pop up window?  I tried added some
>> random fields under the ‘metadata{}’ name in the config.json file.  While
>> they appear in the ‘About this track’ dialog they don’t appear in the
>> faceted track selector.
>>
>>
>>
>> Also, is there a way I can limit which tracks I want to appear in the
>> faceted track selector?  I want a subset of tracks that can appear in their
>> own faceted track selector with many metadata fields to filter upon similar
>> to the original JBrowse.  How do I do this in JBrowse 2?
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Vaneet
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>

Re: [Gmod-ajax] How to add more fields to faceted selector

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

I don't think so. I'll made a tracking issue for this here
https://github.com/GMOD/jbrowse-components/issues/5472

On Wed, Feb 4, 2026 at 3:34 PM Vaneet Lotay <van...@uc...>
wrote:

> Hey Colin,
>
>
>
> Just a follow up to this old topic…thank you for the info by the way!  Is
> there any way to search other fields in the faceted track selector besides
> the track name?
>
>
>
> I realize that when there are metadata attributes that are shared across
> more then 5 tracks those attributes do appear as facets and you can click
> on the facet filters to filter out the results by their values.  However,
> what I’m wondering is there any way to search those additional facets on
> their values from the main search bar of the faceted track selector, or
> does it only simply search the tracknames?
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* October 12, 2025 7:29 AM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmod-ajax <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] How to add more fields to faceted selector
>
>
>
> [△EXTERNAL]
>
>
>
> The basic idea for the faceted track selector is that any "top level"
> entry in the track metadata becomes searchable in the track metadata.
> Example
>
>
>
> {
>       "type": "VariantTrack",
>       "trackId": "volvox_test_vcf",
>       "metadata": {
>         "thing here": "hello"
>       },
>       "name": "volvox 1000genomes vcf",
>       "assemblyNames": ["volvox"],
>       "category": ["Variants"],
>       "adapter": {
>         "type": "VcfTabixAdapter",
>         "uri": "volvox.test.vcf.gz"
>       }
>     },
>
>
>
> That will make "thing here" a column and a facet filter, but also note
> that it filters out "sparse" metadata columns by default, so it only shows
> metadata that is shared across >5 tracks as a facet (arbitrary threshold)
>
>
>
> You can toggle "Show sparse metadata columns" to show facets for even
> metadata not shared by 5 tracks
>
>
>
>
>
>
>
> There is no notion of only a subset of tracks appearing in the faceted
> selector currently
>
>
>
> -Colin
>
>
>
> On Wed, Oct 8, 2025 at 5:16 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hi,
>
>
>
> There is documentation for adding the field ‘category’ as an active field
> to the faceted track selector.  How do you add more fields to that so they
> can be used to filter tracks for in that pop up window?  I tried added some
> random fields under the ‘metadata{}’ name in the config.json file.  While
> they appear in the ‘About this track’ dialog they don’t appear in the
> faceted track selector.
>
>
>
> Also, is there a way I can limit which tracks I want to appear in the
> faceted track selector?  I want a subset of tracks that can appear in their
> own faceted track selector with many metadata fields to filter upon similar
> to the original JBrowse.  How do I do this in JBrowse 2?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Re: [Gmod-ajax] How to add more fields to faceted selector

[Vaneet L. <van...@uc...>]

Hey Colin,

Just a follow up to this old topic…thank you for the info by the way!  Is there any way to search other fields in the faceted track selector besides the track name?

I realize that when there are metadata attributes that are shared across more then 5 tracks those attributes do appear as facets and you can click on the facet filters to filter out the results by their values.  However, what I’m wondering is there any way to search those additional facets on their values from the main search bar of the faceted track selector, or does it only simply search the tracknames?

Thanks,

Vaneet

From: Colin <col...@gm...>
Sent: October 12, 2025 7:29 AM
To: Vaneet Lotay <van...@uc...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: [Gmod-ajax] How to add more fields to faceted selector

[△EXTERNAL]

The basic idea for the faceted track selector is that any "top level" entry in the track metadata becomes searchable in the track metadata.  Example

{
      "type": "VariantTrack",
      "trackId": "volvox_test_vcf",
      "metadata": {
        "thing here": "hello"
      },
      "name": "volvox 1000genomes vcf",
      "assemblyNames": ["volvox"],
      "category": ["Variants"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "volvox.test.vcf.gz"
      }
    },

That will make "thing here" a column and a facet filter, but also note that it filters out "sparse" metadata columns by default, so it only shows metadata that is shared across >5 tracks as a facet (arbitrary threshold)

You can toggle "Show sparse metadata columns" to show facets for even metadata not shared by 5 tracks

[cid:ii_mgnqj31g0]


There is no notion of only a subset of tracks appearing in the faceted selector currently

-Colin

On Wed, Oct 8, 2025 at 5:16 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hi,

There is documentation for adding the field ‘category’ as an active field to the faceted track selector.  How do you add more fields to that so they can be used to filter tracks for in that pop up window?  I tried added some random fields under the ‘metadata{}’ name in the config.json file.  While they appear in the ‘About this track’ dialog they don’t appear in the faceted track selector.

Also, is there a way I can limit which tracks I want to appear in the faceted track selector?  I want a subset of tracks that can appear in their own faceted track selector with many metadata fields to filter upon similar to the original JBrowse.  How do I do this in JBrowse 2?

Thanks,

Vaneet
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] JBrowser

[Miriam H. <mir...@cs...>]

Dear Colin,

Thank you so much for your help and dedication!!

 

I will try to go through the BLAST again and see if I did something wrong there. 

I will be happy to keep in touch with the primer design workflow if I can work it out, but please note that I am not a bioinformatics expert and my knowledge of this field is rather poor but I am happy to contribute with what I can!!

 

Cheers and have a nice day,

 

Miriam

 

De: Colin [mailto:col...@gm...] 
Enviado el: jueves, 15 de enero de 2026 20:54
Para: Miriam Hampel <mir...@cs...>
CC: gmo...@li...
Asunto: Re: [Gmod-ajax] JBrowser

 

Hi Mirian

 

I can see that the file referred to in the URL that you posted is indeed blank, so no results will show up in jbrowse

 

For instance, I put the URL you posted through "URLdecode" here https://www.urldecoder.org/ (converts the percent signs back to ASCII)

 

Resulting urldecoded url

https://genome.atlasea.fr/donax_trunculus/jbrowse/?data=data/donax_trunculus_ass2.0 <https://genome.atlasea.fr/donax_trunculus/jbrowse/?data=data/donax_trunculus_ass2.0&loc=CAXWYC010000118.1:19997..32258&addStores.blast.type=JBrowse/Store/SeqFeature/GFF3&addStores.blast.urlTemplate=https://genome.atlasea.fr/donax_trunculus/blast/tmp/blast_donax_trunculus/blast_donax_trunculus-212852475369675fb5748a57-50272032/blast_donax_trunculus-212852475369675fb5748a57-50272032.gff3&addTracks.blast.label=Blast> &loc=CAXWYC010000118.1:19997..32258&addStores.blast.type=JBrowse/Store/SeqFeature/GFF3&addStores.blast.urlTemplate=https://genome.atlasea.fr/donax_trunculus/blast/tmp/blast_donax_trunculus/blast_donax_trunculus-212852475369675fb5748a57-50272032/blast_donax_trunculus-212852475369675fb5748a57-50272032.gff3&addTracks.blast.label=Blast results&addTracks.blast.type=JBrowse/View/Track/HTMLFeatures&addTracks.blast.store=blast&tracks=Blast results&highlight=

 

This makes it easier to see GFF3 file that is being dynamically referred to for BLAST hits:

https://genome.atlasea.fr/donax_trunculus/blast/tmp/blast_donax_trunculus/blast_donax_trunculus-212852475369675fb5748a57-50272032/blast_donax_trunculus-212852475369675fb5748a57-50272032.gff3

 

And that file is empty

 

JBrowse does not have a way of 'warning' the user if the contents of a track are empty, though this is something that sometimes gets discussed. But in any case, you may need to BLAST again to find the results

 

Just as an aside: I am also interested in these primer design workflows, it might be good if we make some specialized features for this, but note that most of our efforts are for JBrowse 2 now (the link you posted in JBrowse 1)

 

Hope that helps,

-Colin

 

On Wed, Jan 14, 2026 at 7:11 AM Miriam Hampel <mir...@cs... <mailto:mir...@cs...> > wrote:

Hello,

I am new to this list as I was trying to visualize HSPs and finally design primers for D trunculus catalase expression analysis through PCR

I have tblastn-ed the Ruditapes decusatus protein sequence for catalase on the D trunculus blast link: https://genome.atlasea.fr/donax_trunculus/blast/

And I got an output with two significant hits:

Sequence ID                                                     Bitscore               E-value Interpretation

CAXWYC010000118.1 (scaffold)               307                        5e-92     ⭐ Primary catalase locus

OZ187424.1 (chromosome 4)                    126                        9e-30     Partial / duplicated / pseudogene fragment

 

And I am recommended to use the first for catalase primer design for RT qPCR in Donax trunculus. When I click on the corresponding link I am led to JBrowser

https://genome.atlasea.fr/donax_trunculus/jbrowse/?data=data%2Fdonax_trunculus_ass2.0&loc=CAXWYC010000118.1%3A20000..32261&addStores.blast.type=JBrowse%2FStore%2FSeqFeature%2FGFF3&addStores.blast.urlTemplate=https%3A%2F%2Fgenome.atlasea.fr%2Fdonax_trunculus%2Fblast%2Ftmp%2Fblast_donax_trunculus%2Fblast_donax_trunculus-212852475369675fb5748a57-50272032%2Fblast_donax_trunculus-212852475369675fb5748a57-50272032.gff3&addTracks.blast.label=Blast%20results&addTracks.blast.type=JBrowse%2FView%2FTrack%2FHTMLFeatures&addTracks.blast.store=blast&tracks=Blast%20results&highlight=

 

Here I am told to zoom in to see blocks corresponding to HSPs, but as much as I zoom, I cannot see any blocks. Does anybody know what I am doing wrong?

Thank you very much,

All the best

Miriam Hampel

 

_______________________________________________
Gmod-ajax mailing list
Gmo...@li... <mailto:Gmo...@li...> 
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] JBrowser

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

Hi Mirian

I can see that the file referred to in the URL that you posted is indeed
blank, so no results will show up in jbrowse

For instance, I put the URL you posted through "URLdecode" here
https://www.urldecoder.org/ (converts the percent signs back to ASCII)

Resulting urldecoded url
https://genome.atlasea.fr/donax_trunculus/jbrowse/?data=data/donax_trunculus_ass2.0&loc=CAXWYC010000118.1:19997..32258&addStores.blast.type=JBrowse/Store/SeqFeature/GFF3&addStores.blast.urlTemplate=https://genome.atlasea.fr/donax_trunculus/blast/tmp/blast_donax_trunculus/blast_donax_trunculus-212852475369675fb5748a57-50272032/blast_donax_trunculus-212852475369675fb5748a57-50272032.gff3&addTracks.blast.label=Blast
results&addTracks.blast.type=JBrowse/View/Track/HTMLFeatures&addTracks.blast.store=blast&tracks=Blast
results&highlight=

This makes it easier to see GFF3 file that is being dynamically referred to
for BLAST hits:
https://genome.atlasea.fr/donax_trunculus/blast/tmp/blast_donax_trunculus/blast_donax_trunculus-212852475369675fb5748a57-50272032/blast_donax_trunculus-212852475369675fb5748a57-50272032.gff3

And that file is empty

JBrowse does not have a way of 'warning' the user if the contents of a
track are empty, though this is something that sometimes gets discussed.
But in any case, you may need to BLAST again to find the results

Just as an aside: I am also interested in these primer design workflows, it
might be good if we make some specialized features for this, but note that
most of our efforts are for JBrowse 2 now (the link you posted in JBrowse 1)

Hope that helps,
-Colin

On Wed, Jan 14, 2026 at 7:11 AM Miriam Hampel <mir...@cs...> wrote:

> Hello,
>
> I am new to this list as I was trying to visualize HSPs and finally design
> primers for D trunculus catalase expression analysis through PCR
>
> I have tblastn-ed the Ruditapes decusatus protein sequence for catalase on
> the D trunculus blast link:
> https://genome.atlasea.fr/donax_trunculus/blast/
>
> And I got an output with two significant hits:
>
> Sequence ID
> Bitscore               E-value Interpretation
>
> CAXWYC010000118.1 (scaffold)               307
> 5e-92     ⭐ Primary catalase locus
>
> OZ187424.1 (chromosome 4)                    126
> 9e-30     Partial / duplicated / pseudogene fragment
>
>
>
> And I am recommended to use the first for catalase primer design for RT
> qPCR in Donax trunculus. When I click on the corresponding link I am led to
> JBrowser
>
>
> https://genome.atlasea.fr/donax_trunculus/jbrowse/?data=data%2Fdonax_trunculus_ass2.0&loc=CAXWYC010000118.1%3A20000..32261&addStores.blast.type=JBrowse%2FStore%2FSeqFeature%2FGFF3&addStores.blast.urlTemplate=https%3A%2F%2Fgenome.atlasea.fr%2Fdonax_trunculus%2Fblast%2Ftmp%2Fblast_donax_trunculus%2Fblast_donax_trunculus-212852475369675fb5748a57-50272032%2Fblast_donax_trunculus-212852475369675fb5748a57-50272032.gff3&addTracks.blast.label=Blast%20results&addTracks.blast.type=JBrowse%2FView%2FTrack%2FHTMLFeatures&addTracks.blast.store=blast&tracks=Blast%20results&highlight
> =
>
>
>
> Here I am told to zoom in to see blocks corresponding to HSPs, but as much
> as I zoom, I cannot see any blocks. Does anybody know what I am doing wrong?
>
> Thank you very much,
>
> All the best
>
> Miriam Hampel
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowser

[Miriam H. <mir...@cs...>]

Hello,

I am new to this list as I was trying to visualize HSPs and finally design primers for D trunculus catalase expression analysis through PCR

I have tblastn-ed the Ruditapes decusatus protein sequence for catalase on the D trunculus blast link: https://genome.atlasea.fr/donax_trunculus/blast/

And I got an output with two significant hits:

Sequence ID                                                     Bitscore               E-value Interpretation

CAXWYC010000118.1 (scaffold)               307                        5e-92     ⭐ Primary catalase locus

OZ187424.1 (chromosome 4)                    126                        9e-30     Partial / duplicated / pseudogene fragment

 

And I am recommended to use the first for catalase primer design for RT qPCR in Donax trunculus. When I click on the corresponding link I am led to JBrowser

https://genome.atlasea.fr/donax_trunculus/jbrowse/?data=data%2Fdonax_trunculus_ass2.0&loc=CAXWYC010000118.1%3A20000..32261&addStores.blast.type=JBrowse%2FStore%2FSeqFeature%2FGFF3&addStores.blast.urlTemplate=https%3A%2F%2Fgenome.atlasea.fr%2Fdonax_trunculus%2Fblast%2Ftmp%2Fblast_donax_trunculus%2Fblast_donax_trunculus-212852475369675fb5748a57-50272032%2Fblast_donax_trunculus-212852475369675fb5748a57-50272032.gff3&addTracks.blast.label=Blast%20results&addTracks.blast.type=JBrowse%2FView%2FTrack%2FHTMLFeatures&addTracks.blast.store=blast&tracks=Blast%20results&highlight=

 

Here I am told to zoom in to see blocks corresponding to HSPs, but as much as I zoom, I cannot see any blocks. Does anybody know what I am doing wrong?

Thank you very much,

All the best

Miriam Hampel

 

Re: [Gmod-ajax] JBrowse2 sorting track categories with HTML or otherwise?

[Vaneet L. <van...@uc...>]

Thank you so much for your feedback Colin! It all makes sense now.

Vaneet

From: Colin <col...@gm...>
Sent: December 1, 2025 10:33 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: JBrowse2 sorting track categories with HTML or otherwise?

[△EXTERNAL]

>Thank you for adding that feature so quickly, I really appreciate it! From the name of the add-on, I’m going to assume it does what I was talking about from the previous JBrowse?  It allows HTML to be added to track names and then in turn decodes the HTML so it doesn’t visibly show up, is that correct? Or is it a different behaviour?

Yes, if you make invisible html, it will not show up, but can affect sorting. Note that visible HTML will show up. The HTML decoding was already available for track names but the link i sent added it for track categories also

>.  I thought the best way was to create a new .json file via the script that contains the new MultiBigWig track and use the add-track-json command to add that ‘track JSON’ file to the main config.json with all the other tracks.  Is that the best way or is there a better way to do it via the command-line or a different command?

That is a fine way to do it. I encourage making custom scripts to edit the config.json, it is challenging to encode every possible situation into the @jbrowse/cli tool. You also  don't even really have to use add-track-json if you want, you can just write a script to directly edit the config.json

>When added this seems to draw the track using the ‘multirowxy’ renderer type.  My primary question here is how can I change the configuration to draw the track using one of the other renderer types (xyplot, multirowdensity, multiline, multirowline)?  I’m specifically looking to draw it as an xyplot but I’d be interested in how to configure all of the types.  Do I need to change the adapter type?

Example of this here https://github.com/GMOD/jbrowse-components/discussions/3879#discussioncomment-6855563

-Colin


On Mon, Dec 1, 2025 at 1:44 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hey Colin,

Thank you for adding that feature so quickly, I really appreciate it!

From the name of the add-on, I’m going to assume it does what I was talking about from the previous JBrowse?  It allows HTML to be added to track names and then in turn decodes the HTML so it doesn’t visibly show up, is that correct? Or is it a different behaviour?

While we’re discussing JBrowse features, I need some help with Multi-Quantitative tracks; we can always discuss in an online meeting if that works better.  I needed a way to add some MultiBigWig tracks via command-line as I’m using a script so I didn’t want to do it the manual way of entering a new track stanza into the main config.json file.  I thought the best way was to create a new .json file via the script that contains the new MultiBigWig track and use the add-track-json command to add that ‘track JSON’ file to the main config.json with all the other tracks.  Is that the best way or is there a better way to do it via the command-line or a different command?

Anyways, when configuring the track, I followed what was covered in the documentation which uses the MultiWiggleAdapter:

https://jbrowse.org/jb2/docs/config_guides/multiquantitative_track/

When added this seems to draw the track using the ‘multirowxy’ renderer type.  My primary question here is how can I change the configuration to draw the track using one of the other renderer types (xyplot, multirowdensity, multiline, multirowline)?  I’m specifically looking to draw it as an xyplot but I’d be interested in how to configure all of the types.  Do I need to change the adapter type?

Thanks,

Vaneet
From: Colin <col...@gm...<mailto:col...@gm...>>
Sent: November 29, 2025 5:55 PM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmod-ajax <gmo...@li...<mailto:gmo...@li...>>
Subject: Re: JBrowse2 sorting track categories with HTML or otherwise?

[△EXTERNAL]

Hi Vaneet,
I made a change here https://github.com/GMOD/jbrowse-components/pull/5264 that may help with this. It should be out in the next release, which i'm hoping won't be too long

You can try it with

jbrowse create --nightly newinstance


-Colin

On Wed, Nov 26, 2025 at 2:53 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hi all,

In the original JBrowse, when I had a large assortment of tracks and I wanted to sort them in an order other then alphabetical or the position in the config file from where they were added, I used HTML tags in the track names.  Basically ‘<span>’ with the name attribute being given a number to assign the order of the track in the category it belongs to.  I did the same for track categories.

In JBrowse2 I’ve tried the same technique for track names, and it works by decoding the HTML tags and not actually showing the raw HTML in the visible track names.  This method does not work for categories when I try it as the HTML is not decoded and just shown as is in the category name.  So,  does anyone know a better way to sort categories besides alphabetical order?  This becomes relevant where for Xenopus I’m attempting to order categories by development stage not stage # so alphabetical won’t work.  Please let me know if there’s a better way to do this in JBrowse2.

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

Re: [Gmod-ajax] JBrowse2 sorting track categories with HTML or otherwise?

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

>Thank you for adding that feature so quickly, I really appreciate it! From
the name of the add-on, I’m going to assume it does what I was talking
about from the previous JBrowse?  It allows HTML to be added to track names
and then in turn decodes the HTML so it doesn’t visibly show up, is that
correct? Or is it a different behaviour?

Yes, if you make invisible html, it will not show up, but can affect
sorting. Note that visible HTML will show up. The HTML decoding was already
available for track names but the link i sent added it for track categories
also

>.  I thought the best way was to create a new .json file via the script
that contains the new MultiBigWig track and use the add-track-json command
to add that ‘track JSON’ file to the main config.json with all the other
tracks.  Is that the best way or is there a better way to do it via the
command-line or a different command?

That is a fine way to do it. I encourage making custom scripts to edit
the config.json, it is challenging to encode every possible situation into
the @jbrowse/cli tool. You also  don't even really have to use
add-track-json if you want, you can just write a script to directly edit
the config.json

>When added this seems to draw the track using the ‘multirowxy’ renderer
type.  My primary question here is how can I change the configuration to
draw the track using one of the other renderer types (xyplot,
multirowdensity, multiline, multirowline)?  I’m specifically looking to
draw it as an xyplot but I’d be interested in how to configure all of the
types.  Do I need to change the adapter type?



Example of this here
https://github.com/GMOD/jbrowse-components/discussions/3879#discussioncomment-6855563


-Colin


On Mon, Dec 1, 2025 at 1:44 PM Vaneet Lotay <van...@uc...>
wrote:

> Hey Colin,
>
>
>
> Thank you for adding that feature so quickly, I really appreciate it!
>
>
>
> From the name of the add-on, I’m going to assume it does what I was
> talking about from the previous JBrowse?  It allows HTML to be added to
> track names and then in turn decodes the HTML so it doesn’t visibly show
> up, is that correct? Or is it a different behaviour?
>
>
>
> While we’re discussing JBrowse features, I need some help with
> Multi-Quantitative tracks; we can always discuss in an online meeting if
> that works better.  I needed a way to add some MultiBigWig tracks via
> command-line as I’m using a script so I didn’t want to do it the manual way
> of entering a new track stanza into the main config.json file.  I thought
> the best way was to create a new .json file via the script that contains
> the new MultiBigWig track and use the add-track-json command to add that
> ‘track JSON’ file to the main config.json with all the other tracks.  Is
> that the best way or is there a better way to do it via the command-line or
> a different command?
>
>
>
> Anyways, when configuring the track, I followed what was covered in the
> documentation which uses the MultiWiggleAdapter:
>
>
>
> https://jbrowse.org/jb2/docs/config_guides/multiquantitative_track/
>
>
>
> When added this seems to draw the track using the ‘multirowxy’ renderer
> type.  My primary question here is how can I change the configuration to
> draw the track using one of the other renderer types (xyplot,
> multirowdensity, multiline, multirowline)?  I’m specifically looking to
> draw it as an xyplot but I’d be interested in how to configure all of the
> types.  Do I need to change the adapter type?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
> *From:* Colin <col...@gm...>
> *Sent:* November 29, 2025 5:55 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmod-ajax <gmo...@li...>
> *Subject:* Re: JBrowse2 sorting track categories with HTML or otherwise?
>
>
>
> [△EXTERNAL]
>
>
>
> Hi Vaneet,
>
> I made a change here https://github.com/GMOD/jbrowse-components/pull/5264
> that may help with this. It should be out in the next release, which i'm
> hoping won't be too long
>
>
>
> You can try it with
>
>
>
> jbrowse create --nightly newinstance
>
>
>
>
>
> -Colin
>
>
>
> On Wed, Nov 26, 2025 at 2:53 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hi all,
>
>
>
> In the original JBrowse, when I had a large assortment of tracks and I
> wanted to sort them in an order other then alphabetical or the position in
> the config file from where they were added, I used HTML tags in the track
> names.  Basically ‘<span>’ with the name attribute being given a number to
> assign the order of the track in the category it belongs to.  I did the
> same for track categories.
>
>
>
> In JBrowse2 I’ve tried the same technique for track names, and it works by
> decoding the HTML tags and not actually showing the raw HTML in the visible
> track names.  This method does not work for categories when I try it as the
> HTML is not decoded and just shown as is in the category name.  So,  does
> anyone know a better way to sort categories besides alphabetical order?
> This becomes relevant where for Xenopus I’m attempting to order categories
> by development stage not stage # so alphabetical won’t work.  Please let me
> know if there’s a better way to do this in JBrowse2.
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
>
>
>
>

Re: [Gmod-ajax] JBrowse2 sorting track categories with HTML or otherwise?

[Vaneet L. <van...@uc...>]

Hey Colin,

Thank you for adding that feature so quickly, I really appreciate it!

From the name of the add-on, I’m going to assume it does what I was talking about from the previous JBrowse?  It allows HTML to be added to track names and then in turn decodes the HTML so it doesn’t visibly show up, is that correct? Or is it a different behaviour?

While we’re discussing JBrowse features, I need some help with Multi-Quantitative tracks; we can always discuss in an online meeting if that works better.  I needed a way to add some MultiBigWig tracks via command-line as I’m using a script so I didn’t want to do it the manual way of entering a new track stanza into the main config.json file.  I thought the best way was to create a new .json file via the script that contains the new MultiBigWig track and use the add-track-json command to add that ‘track JSON’ file to the main config.json with all the other tracks.  Is that the best way or is there a better way to do it via the command-line or a different command?

Anyways, when configuring the track, I followed what was covered in the documentation which uses the MultiWiggleAdapter:

https://jbrowse.org/jb2/docs/config_guides/multiquantitative_track/

When added this seems to draw the track using the ‘multirowxy’ renderer type.  My primary question here is how can I change the configuration to draw the track using one of the other renderer types (xyplot, multirowdensity, multiline, multirowline)?  I’m specifically looking to draw it as an xyplot but I’d be interested in how to configure all of the types.  Do I need to change the adapter type?

Thanks,

Vaneet
From: Colin <col...@gm...>
Sent: November 29, 2025 5:55 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: JBrowse2 sorting track categories with HTML or otherwise?

[△EXTERNAL]

Hi Vaneet,
I made a change here https://github.com/GMOD/jbrowse-components/pull/5264 that may help with this. It should be out in the next release, which i'm hoping won't be too long

You can try it with

jbrowse create --nightly newinstance


-Colin

On Wed, Nov 26, 2025 at 2:53 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hi all,

In the original JBrowse, when I had a large assortment of tracks and I wanted to sort them in an order other then alphabetical or the position in the config file from where they were added, I used HTML tags in the track names.  Basically ‘<span>’ with the name attribute being given a number to assign the order of the track in the category it belongs to.  I did the same for track categories.

In JBrowse2 I’ve tried the same technique for track names, and it works by decoding the HTML tags and not actually showing the raw HTML in the visible track names.  This method does not work for categories when I try it as the HTML is not decoded and just shown as is in the category name.  So,  does anyone know a better way to sort categories besides alphabetical order?  This becomes relevant where for Xenopus I’m attempting to order categories by development stage not stage # so alphabetical won’t work.  Please let me know if there’s a better way to do this in JBrowse2.

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

Re: [Gmod-ajax] JBrowse2 sorting track categories with HTML or otherwise?

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

Hi Vaneet,
I made a change here https://github.com/GMOD/jbrowse-components/pull/5264
that may help with this. It should be out in the next release, which i'm
hoping won't be too long

You can try it with

jbrowse create --nightly newinstance


-Colin

On Wed, Nov 26, 2025 at 2:53 PM Vaneet Lotay <van...@uc...>
wrote:

> Hi all,
>
>
>
> In the original JBrowse, when I had a large assortment of tracks and I
> wanted to sort them in an order other then alphabetical or the position in
> the config file from where they were added, I used HTML tags in the track
> names.  Basically ‘<span>’ with the name attribute being given a number to
> assign the order of the track in the category it belongs to.  I did the
> same for track categories.
>
>
>
> In JBrowse2 I’ve tried the same technique for track names, and it works by
> decoding the HTML tags and not actually showing the raw HTML in the visible
> track names.  This method does not work for categories when I try it as the
> HTML is not decoded and just shown as is in the category name.  So,  does
> anyone know a better way to sort categories besides alphabetical order?
> This becomes relevant where for Xenopus I’m attempting to order categories
> by development stage not stage # so alphabetical won’t work.  Please let me
> know if there’s a better way to do this in JBrowse2.
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
>
>
>

[Gmod-ajax] JBrowse2 sorting track categories with HTML or otherwise?

[Vaneet L. <van...@uc...>]

Hi all,

In the original JBrowse, when I had a large assortment of tracks and I wanted to sort them in an order other then alphabetical or the position in the config file from where they were added, I used HTML tags in the track names.  Basically '<span>' with the name attribute being given a number to assign the order of the track in the category it belongs to.  I did the same for track categories.

In JBrowse2 I've tried the same technique for track names, and it works by decoding the HTML tags and not actually showing the raw HTML in the visible track names.  This method does not work for categories when I try it as the HTML is not decoded and just shown as is in the category name.  So,  does anyone know a better way to sort categories besides alphabetical order?  This becomes relevant where for Xenopus I'm attempting to order categories by development stage not stage # so alphabetical won't work.  Please let me know if there's a better way to do this in JBrowse2.

Thanks,

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

Re: [Gmod-ajax] How to add more fields to faceted selector

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

The basic idea for the faceted track selector is that any "top level" entry
in the track metadata becomes searchable in the track metadata.  Example

{
      "type": "VariantTrack",
      "trackId": "volvox_test_vcf",
      "metadata": {
        "thing here": "hello"
      },
      "name": "volvox 1000genomes vcf",
      "assemblyNames": ["volvox"],
      "category": ["Variants"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "volvox.test.vcf.gz"
      }
    },

That will make "thing here" a column and a facet filter, but also note that
it filters out "sparse" metadata columns by default, so it only shows
metadata that is shared across >5 tracks as a facet (arbitrary threshold)

You can toggle "Show sparse metadata columns" to show facets for even
metadata not shared by 5 tracks

[image: image.png]



There is no notion of only a subset of tracks appearing in the faceted
selector currently

-Colin

On Wed, Oct 8, 2025 at 5:16 PM Vaneet Lotay <van...@uc...>
wrote:

> Hi,
>
>
>
> There is documentation for adding the field ‘category’ as an active field
> to the faceted track selector.  How do you add more fields to that so they
> can be used to filter tracks for in that pop up window?  I tried added some
> random fields under the ‘metadata{}’ name in the config.json file.  While
> they appear in the ‘About this track’ dialog they don’t appear in the
> faceted track selector.
>
>
>
> Also, is there a way I can limit which tracks I want to appear in the
> faceted track selector?  I want a subset of tracks that can appear in their
> own faceted track selector with many metadata fields to filter upon similar
> to the original JBrowse.  How do I do this in JBrowse 2?
>
>
>
> Thanks,
>
>
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] How to add more fields to faceted selector

[Vaneet L. <van...@uc...>]

Hi,

There is documentation for adding the field 'category' as an active field to the faceted track selector.  How do you add more fields to that so they can be used to filter tracks for in that pop up window?  I tried added some random fields under the 'metadata{}' name in the config.json file.  While they appear in the 'About this track' dialog they don't appear in the faceted track selector.

Also, is there a way I can limit which tracks I want to appear in the faceted track selector?  I want a subset of tracks that can appear in their own faceted track selector with many metadata fields to filter upon similar to the original JBrowse.  How do I do this in JBrowse 2?

Thanks,

Vaneet

Re: [Gmod-ajax] Gene search result remains

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

(note that you can also change the entire "session title" in the same way
by clicking where it says "New session ..." on the top level blue
navigation bar)


-Colin

On Fri, Jun 27, 2025 at 3:07 PM Colin <col...@gm...> wrote:

> I don't believe this is currently possible. However, if this is just for
> screenshot purposes or just to remember what was searched, note that you
> can manually edit the "View title" in the purple bar view header.
>
> For example, see the screenshot below: It says "My custom text here" in
> the view header, just due to me clicking the view header text and typing to
> make my own custom title
>
> [image: image.png]
>
> Hope that helps
>
> -Colin
>
> On Fri, Jun 27, 2025 at 11:58 AM Vaneet Lotay <van...@uc...>
> wrote:
>
>> Hi,
>>
>>
>>
>> My PI was curious about something in JBrowse2.  When you enter a search
>> result in the location box and visit the location where the gene is in the
>> genome, is it possible to allow the search results to remain in the search
>> box instead of it switching automatically to the genome coordinates?  Or
>> perhaps can the gene search result remain anywhere in that top panel after
>> you've visited your gene of interest.  I assume this isn't possible but
>> just thought I'd ask if there's a plugin for it perhaps.
>>
>> Thanks,
>>
>> Vaneet
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] Gene search result remains

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

I don't believe this is currently possible. However, if this is just for
screenshot purposes or just to remember what was searched, note that you
can manually edit the "View title" in the purple bar view header.

For example, see the screenshot below: It says "My custom text here" in the
view header, just due to me clicking the view header text and typing to
make my own custom title

[image: image.png]

Hope that helps

-Colin

On Fri, Jun 27, 2025 at 11:58 AM Vaneet Lotay <van...@uc...>
wrote:

> Hi,
>
>
>
> My PI was curious about something in JBrowse2.  When you enter a search
> result in the location box and visit the location where the gene is in the
> genome, is it possible to allow the search results to remain in the search
> box instead of it switching automatically to the genome coordinates?  Or
> perhaps can the gene search result remain anywhere in that top panel after
> you've visited your gene of interest.  I assume this isn't possible but
> just thought I'd ask if there's a plugin for it perhaps.
>
> Thanks,
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Gene search result remains

[Vaneet L. <van...@uc...>]

Hi,



My PI was curious about something in JBrowse2.  When you enter a search result in the location box and visit the location where the gene is in the genome, is it possible to allow the search results to remain in the search box instead of it switching automatically to the genome coordinates?  Or perhaps can the gene search result remain anywhere in that top panel after you've visited your gene of interest.  I assume this isn't possible but just thought I'd ask if there's a plugin for it perhaps.

Thanks,

Vaneet

Re: [Gmod-ajax] JBrowse2 VCF track

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

Currently there is no option for this. Potential could add it though!

If you can make a github issue for it that would be great
-Colin

On Thu, May 29, 2025 at 2:54 PM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> I'd like to know whether it is possible to turn off the rendering of the
> "genotype" column for a VCF track in the feature details in the track
> configuration. Looks like as a user viewing the track, we can click the
> "columns" button to select the columns to show. But is there a way to
> selectively hide columns in the backend of track configuration, so by
> default users would only see certain columns of VCF INFO fields?
>
> For an example, see attached screenshot. We'd like to show only "sample"
> and "GT" by default, no "genotype" column.
>
> Thanks!
>
> Ke
> [image: Screenshot 2025-05-29 at 1.48.16 PM.png]
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse2 VCF track

[Ke J. <bio...@gm...>]

Hi,

I'd like to know whether it is possible to turn off the rendering of the
"genotype" column for a VCF track in the feature details in the track
configuration. Looks like as a user viewing the track, we can click the
"columns" button to select the columns to show. But is there a way to
selectively hide columns in the backend of track configuration, so by
default users would only see certain columns of VCF INFO fields?

For an example, see attached screenshot. We'd like to show only "sample"
and "GT" by default, no "genotype" column.

Thanks!

Ke
[image: Screenshot 2025-05-29 at 1.48.16 PM.png]

Re: [Gmod-ajax] JBrowse subfeatures repeating bug?

[Vaneet L. <van...@uc...>]

Hey Colin,

Here’s an example for the hhat gene:

https://jbrowse.xenbase.org/XenJBrowse/?data=data%2Fxt10_0&loc=Chr5%3A15519428..15720936&tracks=DNA%2CXT10_0_Xenbase%2CgRNAs&highlight=

If you click on the gene models and then ‘show subfeatures’, you can see the UTR being repeated several times, which isn’t present in the GFF3 file itself.  Most models with UTRs show this repeated issue.

Thanks,

Vaneet

From: Colin <col...@gm...>
Sent: May 12, 2025 1:35 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: JBrowse subfeatures repeating bug?

[△EXTERNAL]

If you can send a link it may help

-Colin

On Mon, May 12, 2025 at 2:42 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hi Colin,

Have you ever encountered this bug below in JBrowse when using ‘NCBI’ style GFF3s with implied UTRs to be drawn in the JBrowse tracks?

Anyone else ever run into this issue?  I’m just wondering if there’s something that can be done to prevent it from repeating like that.  I can give a direct link to someone if they want to see the issue live and recreate it.

Thanks,

Vaneet

From: Vaneet Lotay
Sent: April 9, 2025 10:51 AM
To: gmo...@li...<mailto:gmo...@li...>
Subject: JBrowse subfeatures repeating bug?

Hi,

I’m not sure if anyone’s already run into this bug before, at least it certainly seems like a bug.  When I click on my gene model in JBrowse, and then click on subfeatures under a given mRNA, the same 3’UTR or 5’UTR segment gets displayed multiple times as duplicates with the same coordinates (screenshot attached).  It doesn’t matter which model I select or even under which species or genome for that matter that it’s under, it always appears repeated like that in the details window.  Here’s a trimmed down version of the hhex.S gene that’s in the screenshot from my GFF3 (column 9 attributes trimmed off) just so it can fit here:

Chr7S   Gnomon  gene    15890549        15902647        .       -       .       ID=XBXL10_1g32594;Name=hhex.S
Chr7S   Gnomon  mRNA    15890549        15902647        .       -       .       ID=XBmRNA61523;Parent=XBXL10_1g32594
Chr7S   Gnomon  exon    15902179        15902647        .       -       .       ID=XBexon785823;Parent=XBmRNA61523
Chr7S   Gnomon  exon    15896206        15896384        .       -       .       ID=XBexon785824;Parent=XBmRNA61523
Chr7S   Gnomon  exon    15894761        15894811        .       -       .       ID=XBexon785825;Parent=XBmRNA61523
Chr7S   Gnomon  exon    15890549        15891175        .       -       .       ID=XBexon785826;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15902179        15902551        .       -       0       ID=XBcds718348;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15896206        15896384        .       -       2       ID=XBcds718348;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15894761        15894811        .       -       0       ID=XBcds718348;Parent=XBmRNA61523
Chr7S   Gnomon  CDS     15890948        15891175        .       -       0       ID=XBcds718348;Parent=XBmRNA61523

I have this setting enabled in my track to draw out the ‘implied’ UTRs which aren’t directly supplied in the GFF3 file:

        "impliedUTRs" : true,

Has anyone run into this before?  Is it a technical bug?  Why is it happening?

Thanks,

Vaneet

Re: [Gmod-ajax] JBrowse subfeatures repeating bug?

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

If you can send a link it may help

-Colin

On Mon, May 12, 2025 at 2:42 PM Vaneet Lotay <van...@uc...>
wrote:

> Hi Colin,
>
>
>
> Have you ever encountered this bug below in JBrowse when using ‘NCBI’
> style GFF3s with implied UTRs to be drawn in the JBrowse tracks?
>
>
>
> Anyone else ever run into this issue?  I’m just wondering if there’s
> something that can be done to prevent it from repeating like that.  I can
> give a direct link to someone if they want to see the issue live and
> recreate it.
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *From:* Vaneet Lotay
> *Sent:* April 9, 2025 10:51 AM
> *To:* gmo...@li...
> *Subject:* JBrowse subfeatures repeating bug?
>
>
>
> Hi,
>
>
>
> I’m not sure if anyone’s already run into this bug before, at least it
> certainly seems like a bug.  When I click on my gene model in JBrowse, and
> then click on subfeatures under a given mRNA, the same 3’UTR or 5’UTR
> segment gets displayed multiple times as duplicates with the same
> coordinates (screenshot attached).  It doesn’t matter which model I select
> or even under which species or genome for that matter that it’s under, it
> always appears repeated like that in the details window.  Here’s a trimmed
> down version of the hhex.S gene that’s in the screenshot from my GFF3
> (column 9 attributes trimmed off) just so it can fit here:
>
>
>
> Chr7S   Gnomon  gene    15890549        15902647        .       -
> .       ID=XBXL10_1g32594;Name=hhex.S
>
> Chr7S   Gnomon  mRNA    15890549        15902647        .       -
> .       ID=XBmRNA61523;Parent=XBXL10_1g32594
>
> Chr7S   Gnomon  exon    15902179        15902647        .       -
> .       ID=XBexon785823;Parent=XBmRNA61523
>
> Chr7S   Gnomon  exon    15896206        15896384        .       -
> .       ID=XBexon785824;Parent=XBmRNA61523
>
> Chr7S   Gnomon  exon    15894761        15894811        .       -
> .       ID=XBexon785825;Parent=XBmRNA61523
>
> Chr7S   Gnomon  exon    15890549        15891175        .       -
> .       ID=XBexon785826;Parent=XBmRNA61523
>
> Chr7S   Gnomon  CDS     15902179        15902551        .       -
> 0       ID=XBcds718348;Parent=XBmRNA61523
>
> Chr7S   Gnomon  CDS     15896206        15896384        .       -
> 2       ID=XBcds718348;Parent=XBmRNA61523
>
> Chr7S   Gnomon  CDS     15894761        15894811        .       -
> 0       ID=XBcds718348;Parent=XBmRNA61523
>
> Chr7S   Gnomon  CDS     15890948        15891175        .       -
> 0       ID=XBcds718348;Parent=XBmRNA61523
>
>
>
> I have this setting enabled in my track to draw out the ‘implied’ UTRs
> which aren’t directly supplied in the GFF3 file:
>
>
>
>         "impliedUTRs" : true,
>
>
>
> Has anyone run into this before?  Is it a technical bug?  Why is it
> happening?
>
>
>
> Thanks,
>
>
> Vaneet
>