gmod-ajax — JBrowse list

Re: [Gmod-ajax] JBrowse2 loading human hg38

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

what is the source of "hg38.ncbiRefSeq.gff3.gz"?

-Colin

On Wed, Apr 17, 2024 at 12:36 PM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
>
>
> Not sure if this is a JBrowse issue or one with the human genome or gene
> models, but this being human, it’s a fairly common genome so I though I’d
> ask the community in case they have ran into any issues when loading hg38
> and its gene models.
>
>
>
> So, I loaded the human hg38 version genome assembly (hg38.masked.fa.gz)
> and that worked fine.  I loaded the NCBI RefSeq gene models track (hg38.ncbiRefSeq.gff3.gz)
> for hg38 next and that seemed to load fine.  However, when I go to any of
> the standard chromosomes which have a short sequence ID (chr1, chr2,
> ..etc.) as opposed to the appended longer sequence IDs
> (chr8_KI270815v1_alt, chr9_GL383540v1_alt) I get this error (stack trace):
>
>
>
>
>
> *Error: some features reference other features that do not exist in the
> file (or in the same '###' scope).
> PRAMEF30P,RNU6-1072P,PRAMEF29P,PRAMEF28P,PRAMEF35P,PRAMEF31P,PRAMEF32P,RNU6-771P,MT1XP1,RPL22P3,RNU1-6P,TRV-CAC11-1,PDE4DIPP8,LOC101056699,EIF1AXP1,TRV-CAC13-1,CROCCP4,PDE4DIPP9,TRV-CAC11-2,LOC124903860,RNU1-5P,LOC107985101,RPL29P6,DPPA2P2,RN7SL679P,RPL36AP9,RPL31P12,LOC100131348,SLC25A24P1,NBPF5P,SLC25A24P2,ST13P21,LOC100420170,LOC124904641,LOC107985110,GEMIN2P1,RN7SL372P,LOC645965,MTX1P1,MPTX1,OR10J2P,OR10J7P,OR10J8P,OR10J9P,LOC100996886,PEBP1P3,ST13P19,RNASEH1P3,RNU5A-8P,BPNT2P1,RPL23AP15,H2BU2P,RNA5SP19,RNA5SP18,LOC124900442,FTH1P2,LOC100418822,RPS21P1,MTCYBP14,MTND6P14,MTND5P19,MTND4P10,MTND4LP21,MTND3P8,MTCO3P46,SEPTIN14P21,CICP21,RNU6-747P,FCF1P7,FABP7P1,VN1R17P,OR2AS2P,OR2AS1P*
>
> *_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867
> <_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867>*
>
> *finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856
> <finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856>*
>
> *parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409
> <parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409>*
>
> *getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706
> <getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706>*
>
>
>
> *JBrowse 2.10.3*
>
>
>
> This error was on chr1 but as I said it happens for pretty much any
> standard chromosome I go to.  When I go to the ‘alt’ or ‘random’ sequences
> with the longer sequence names, they seem to load gene models fine.  When I
> check those mentioned gene models in the error, I can’t seem to find
> anything wrong with its references.
>
>
>
> Just wanted to check in case someone has ran into the same error and how
> it was resolved.
>
>
>
> Thanks,
>
>
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse2 loading human hg38

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

Hello,

Not sure if this is a JBrowse issue or one with the human genome or gene models, but this being human, it's a fairly common genome so I though I'd ask the community in case they have ran into any issues when loading hg38 and its gene models.

So, I loaded the human hg38 version genome assembly (hg38.masked.fa.gz) and that worked fine.  I loaded the NCBI RefSeq gene models track (hg38.ncbiRefSeq.gff3.gz) for hg38 next and that seemed to load fine.  However, when I go to any of the standard chromosomes which have a short sequence ID (chr1, chr2, ..etc.) as opposed to the appended longer sequence IDs (chr8_KI270815v1_alt, chr9_GL383540v1_alt) I get this error (stack trace):


Error: some features reference other features that do not exist in the file (or in the same '###' scope). PRAMEF30P,RNU6-1072P,PRAMEF29P,PRAMEF28P,PRAMEF35P,PRAMEF31P,PRAMEF32P,RNU6-771P,MT1XP1,RPL22P3,RNU1-6P,TRV-CAC11-1,PDE4DIPP8,LOC101056699,EIF1AXP1,TRV-CAC13-1,CROCCP4,PDE4DIPP9,TRV-CAC11-2,LOC124903860,RNU1-5P,LOC107985101,RPL29P6,DPPA2P2,RN7SL679P,RPL36AP9,RPL31P12,LOC100131348,SLC25A24P1,NBPF5P,SLC25A24P2,ST13P21,LOC100420170,LOC124904641,LOC107985110,GEMIN2P1,RN7SL372P,LOC645965,MTX1P1,MPTX1,OR10J2P,OR10J7P,OR10J8P,OR10J9P,LOC100996886,PEBP1P3,ST13P19,RNASEH1P3,RNU5A-8P,BPNT2P1,RPL23AP15,H2BU2P,RNA5SP19,RNA5SP18,LOC124900442,FTH1P2,LOC100418822,RPS21P1,MTCYBP14,MTND6P14,MTND5P19,MTND4P10,MTND4LP21,MTND3P8,MTCO3P46,SEPTIN14P21,CICP21,RNU6-747P,FCF1P7,FABP7P1,VN1R17P,OR2AS2P,OR2AS1P
_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867<mailto:_emitAllUnderConstructionFeatures@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:5867>
finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856<mailto:finish@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:4856>
parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409<mailto:parseStringSync@https://jbrowse.xenbase.org/XenJBrowse2/static/js/2202.77c82acb.chunk.js:1:10409>
getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706<mailto:getFeaturesHelper@https://jbrowse.xenbase.org/XenJBrowse2/static/js/5441.c7415ecc.chunk.js:1:1706>

JBrowse 2.10.3

This error was on chr1 but as I said it happens for pretty much any standard chromosome I go to.  When I go to the 'alt' or 'random' sequences with the longer sequence names, they seem to load gene models fine.  When I check those mentioned gene models in the error, I can't seem to find anything wrong with its references.

Just wanted to check in case someone has ran into the same error and how it was resolved.

Thanks,

Vaneet

Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?

[Scott C. <sc...@sc...>]

🤷 I don't know--I haven't tried, that's why I was hedging a bit with my
response. It probably will work. If it doesn't, the other option would be
to write a plugin (which is described lower down on the same page).

On Wed, Apr 10, 2024 at 12:34 PM Vaneet Lotay <van...@uc...>
wrote:

> Well by that logic I suppose you can if you can still call the contents of
> the old field you set to null.  Like for example would I able to do this in
> the formatDetails section below?
>
>
>
>   "formatDetails": {
>     "feature": "jexl:{name:undefined, Gene_symbol:feature.name}"
>   },
>
>
>
> Does the contents of that nullified field get lost if set to null?
>
>
>
> Thanks,
>
>
> Vaneet
>
>
>
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Wednesday, April 10, 2024 12:35 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?
>
>
>
> [△EXTERNAL]
>
>
>
> Hi Vaneet,
>
>
>
> That is documented here:
> https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/
>
> While you can't (I don't think) "rename" a field, you can remove a field
> by setting it to null, and create a new field with a new label, which is
> (again, I think) functionally the same as renaming.
>
>
>
> Scott
>
>
>
>
>
> On Wed, Apr 10, 2024 at 11:19 AM Vaneet Lotay <van...@uc...>
> wrote:
>
> Thanks Scott.  By the way I had another question, how do you change the
> names of the actual fields in the feature details pop up box?  I realize
> there’s a way to change their values, but I didn’t see how to do it for the
> field names themselves. I remember doing it in JBrowse1.  I didn’t define
> some additional fields in my bed file so they show up as field 11, field
> 12, ..etc.
>
>
>
> Vaneet
>
>
>
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Friday, March 29, 2024 10:34 AM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?
>
>
>
> [△EXTERNAL]
>
>
>
> Hi Vaneet,
>
>
>
> You can change the mouseover by providing jexl in the 'display' block (but
> not in the 'render' block), like this:
>
>
>
>  "displays": [
>     {
>       "type": "LinearBasicDisplay",
>       "displayId":
> "Macaca_mulatta_all_genes-LinearBasicDisplay-1711729713263",
>       "mouseover": "jexl:get(feature,'gene_biotype')",
>       "renderer": {
>         "type": "SvgFeatureRenderer",
>         "color1": "jexl:get(feature,'strand')<0?'teal':'darkviolet'",
>         "color3": "#30332E",
>         "maxHeight": 5000
>       }
>     }
>   ]
>
>
>
> Scott
>
>
>
>
>
>
>
>
>
> On Thu, Mar 28, 2024 at 1:35 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello,
>
>
>
> I couldn’t find anything specific in the docs about this but is there
> anyway we can configure what is shown when you hover over a feature in a
> track, like a tooltip?  JBrowse1 had the ‘onClick’ method which I used to
> configure mouse hover functionality, so I’m wondering if that can still be
> used or is there another way to configure feature tooltips?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
>
> GMOD Project Manager (http://gmod.org/)
> 216-392-3087
>
> WormBase Developer (http://wormbase.org/)
>
> Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
>
> VirusSeq Project Manager (https://virusseq-dataportal.ca/)
>
> Human Cancer Models Initiative Project Manager (
> https://hcmi-searchable-catalog.nci.nih.gov/)
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
>
> GMOD Project Manager (http://gmod.org/)
> 216-392-3087
>
> WormBase Developer (http://wormbase.org/)
>
> Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
>
> VirusSeq Project Manager (https://virusseq-dataportal.ca/)
>
> Human Cancer Models Initiative Project Manager (
> https://hcmi-searchable-catalog.nci.nih.gov/)
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)

Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?

[Scott C. <sc...@sc...>]

Hi Vaneet,

That is documented here:
https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/

While you can't (I don't think) "rename" a field, you can remove a field by
setting it to null, and create a new field with a new label, which is
(again, I think) functionally the same as renaming.

Scott


On Wed, Apr 10, 2024 at 11:19 AM Vaneet Lotay <van...@uc...>
wrote:

> Thanks Scott.  By the way I had another question, how do you change the
> names of the actual fields in the feature details pop up box?  I realize
> there’s a way to change their values, but I didn’t see how to do it for the
> field names themselves. I remember doing it in JBrowse1.  I didn’t define
> some additional fields in my bed file so they show up as field 11, field
> 12, ..etc.
>
>
>
> Vaneet
>
>
>
> *From:* Scott Cain <sc...@sc...>
> *Sent:* Friday, March 29, 2024 10:34 AM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmo...@li...
> *Subject:* Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?
>
>
>
> [△EXTERNAL]
>
>
>
> Hi Vaneet,
>
>
>
> You can change the mouseover by providing jexl in the 'display' block (but
> not in the 'render' block), like this:
>
>
>
>  "displays": [
>     {
>       "type": "LinearBasicDisplay",
>       "displayId":
> "Macaca_mulatta_all_genes-LinearBasicDisplay-1711729713263",
>       "mouseover": "jexl:get(feature,'gene_biotype')",
>       "renderer": {
>         "type": "SvgFeatureRenderer",
>         "color1": "jexl:get(feature,'strand')<0?'teal':'darkviolet'",
>         "color3": "#30332E",
>         "maxHeight": 5000
>       }
>     }
>   ]
>
>
>
> Scott
>
>
>
>
>
>
>
>
>
> On Thu, Mar 28, 2024 at 1:35 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello,
>
>
>
> I couldn’t find anything specific in the docs about this but is there
> anyway we can configure what is shown when you hover over a feature in a
> track, like a tooltip?  JBrowse1 had the ‘onClick’ method which I used to
> configure mouse hover functionality, so I’m wondering if that can still be
> used or is there another way to configure feature tooltips?
>
>
>
> Thanks,
>
>
>
> Vaneet
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
>
> GMOD Project Manager (http://gmod.org/)
> 216-392-3087
>
> WormBase Developer (http://wormbase.org/)
>
> Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
>
> VirusSeq Project Manager (https://virusseq-dataportal.ca/)
>
> Human Cancer Models Initiative Project Manager (
> https://hcmi-searchable-catalog.nci.nih.gov/)
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)

Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?

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

Well by that logic I suppose you can if you can still call the contents of the old field you set to null.  Like for example would I able to do this in the formatDetails section below?

  "formatDetails": {
    "feature": "jexl:{name:undefined, Gene_symbol:feature.name}"
  },

Does the contents of that nullified field get lost if set to null?

Thanks,

Vaneet

From: Scott Cain <sc...@sc...>
Sent: Wednesday, April 10, 2024 12:35 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?

[△EXTERNAL]

Hi Vaneet,

That is documented here: https://jbrowse.org/jb2/docs/config_guides/customizing_feature_details/
While you can't (I don't think) "rename" a field, you can remove a field by setting it to null, and create a new field with a new label, which is (again, I think) functionally the same as renaming.

Scott


On Wed, Apr 10, 2024 at 11:19 AM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Thanks Scott.  By the way I had another question, how do you change the names of the actual fields in the feature details pop up box?  I realize there’s a way to change their values, but I didn’t see how to do it for the field names themselves. I remember doing it in JBrowse1.  I didn’t define some additional fields in my bed file so they show up as field 11, field 12, ..etc.

Vaneet

From: Scott Cain <sc...@sc...<mailto:sc...@sc...>>
Sent: Friday, March 29, 2024 10:34 AM
To: Vaneet Lotay <van...@uc...<mailto:van...@uc...>>
Cc: gmo...@li...<mailto:gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?

[△EXTERNAL]

Hi Vaneet,

You can change the mouseover by providing jexl in the 'display' block (but not in the 'render' block), like this:

 "displays": [
    {
      "type": "LinearBasicDisplay",
      "displayId": "Macaca_mulatta_all_genes-LinearBasicDisplay-1711729713263",
      "mouseover": "jexl:get(feature,'gene_biotype')",
      "renderer": {
        "type": "SvgFeatureRenderer",
        "color1": "jexl:get(feature,'strand')<0?'teal':'darkviolet'",
        "color3": "#30332E",
        "maxHeight": 5000
      }
    }
  ]

Scott




On Thu, Mar 28, 2024 at 1:35 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I couldn’t find anything specific in the docs about this but is there anyway we can configure what is shown when you hover over a feature in a track, like a tooltip?  JBrowse1 had the ‘onClick’ method which I used to configure mouse hover functionality, so I’m wondering if that can still be used or is there another way to configure feature tooltips?

Thanks,

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


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott at scottcain dot net
GMOD Project Manager (http://gmod.org/)                            216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/)


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott at scottcain dot net
GMOD Project Manager (http://gmod.org/)                            216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/)

Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?

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

Thanks Scott.  By the way I had another question, how do you change the names of the actual fields in the feature details pop up box?  I realize there’s a way to change their values, but I didn’t see how to do it for the field names themselves. I remember doing it in JBrowse1.  I didn’t define some additional fields in my bed file so they show up as field 11, field 12, ..etc.

Vaneet

From: Scott Cain <sc...@sc...>
Sent: Friday, March 29, 2024 10:34 AM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?

[△EXTERNAL]

Hi Vaneet,

You can change the mouseover by providing jexl in the 'display' block (but not in the 'render' block), like this:

 "displays": [
    {
      "type": "LinearBasicDisplay",
      "displayId": "Macaca_mulatta_all_genes-LinearBasicDisplay-1711729713263",
      "mouseover": "jexl:get(feature,'gene_biotype')",
      "renderer": {
        "type": "SvgFeatureRenderer",
        "color1": "jexl:get(feature,'strand')<0?'teal':'darkviolet'",
        "color3": "#30332E",
        "maxHeight": 5000
      }
    }
  ]

Scott




On Thu, Mar 28, 2024 at 1:35 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I couldn’t find anything specific in the docs about this but is there anyway we can configure what is shown when you hover over a feature in a track, like a tooltip?  JBrowse1 had the ‘onClick’ method which I used to configure mouse hover functionality, so I’m wondering if that can still be used or is there another way to configure feature tooltips?

Thanks,

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


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott at scottcain dot net
GMOD Project Manager (http://gmod.org/)                            216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/)

Re: [Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?

[Scott C. <sc...@sc...>]

Hi Vaneet,

You can change the mouseover by providing jexl in the 'display' block (but
not in the 'render' block), like this:

 "displays": [
    {
      "type": "LinearBasicDisplay",
      "displayId":
"Macaca_mulatta_all_genes-LinearBasicDisplay-1711729713263",
      "mouseover": "jexl:get(feature,'gene_biotype')",
      "renderer": {
        "type": "SvgFeatureRenderer",
        "color1": "jexl:get(feature,'strand')<0?'teal':'darkviolet'",
        "color3": "#30332E",
        "maxHeight": 5000
      }
    }
  ]

Scott




On Thu, Mar 28, 2024 at 1:35 PM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
>
>
> I couldn’t find anything specific in the docs about this but is there
> anyway we can configure what is shown when you hover over a feature in a
> track, like a tooltip?  JBrowse1 had the ‘onClick’ method which I used to
> configure mouse hover functionality, so I’m wondering if that can still be
> used or is there another way to configure feature tooltips?
>
>
>
> Thanks,
>
>
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)

[Gmod-ajax] JBrowse2 tooltips/mouse-hover for features?

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

Hello,

I couldn't find anything specific in the docs about this but is there anyway we can configure what is shown when you hover over a feature in a track, like a tooltip?  JBrowse1 had the 'onClick' method which I used to configure mouse hover functionality, so I'm wondering if that can still be used or is there another way to configure feature tooltips?

Thanks,

Vaneet

Re: [Gmod-ajax] JBrowse2 dynamically changing URL?

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

During normal operation, the session is local to your browser, specifically
using browser localStorage.

 When you use the share button, your session is encrypted, copied to our
server, and then a short url is generated referring to that copy that is
online. We do not not plan to delete sessions and session sgare urls should
be alive as long as we stay online :)

Short faq entry
https://jbrowse.org/jb2/docs/faq/#how-does-the-session-sharing-work-with-shortened-urls-work-in-jbrowse-web


-Colin

On Wed, Mar 27, 2024, 12:37 PM Vaneet Lotay <van...@uc...>
wrote:

> Thanks guys for the detailed explanation.  So for sessions....isn't that
> saved local to my browser or is it possible to share it with another user?
> If so how long can the session be shared for before it's removed from the
> server?  Do you have to create a session JSON file to properly store it in
> the server to make sure it doesn't get deleted before sharing it with
> someone?
>
> Vaneet
> ------------------------------
> *From:* Colin <col...@gm...>
> *Sent:* March 27, 2024 9:10 AM
> *To:* Scott Cain <sc...@sc...>
> *Cc:* Vaneet Lotay <van...@uc...>;
> gmo...@li... <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] JBrowse2 dynamically changing URL?
>
> [△EXTERNAL]
>
> Basically what Scott says, but just to add a little more perspective
>
> As a  comparison, JBrowse 1 did have the auto-updating url, and it was a
> relatively simple system that just stored the current "&loc=chr:1-100" type
> location that you are viewing in the url. That was pretty much all that was
> stored...that and tracks and data directory...
>
> With JBrowse 2, we have the ability to have multiple views, and all sorts
> of  2 just became a kind of complex app with multiple views, and each view
> can have subviews (think synteny view) and so it became hard to port over
> the notion of having a simple URL.
>
> I know this is a little unfortunate that the URL bar is not copyable at
> any time, but as Scott said, we do have the "Share" button that lets you
> get shareable URL.
>
> If the Share button was undesirable, and someone really wanted live
> updating URLs they could conceivably....
>
> a) make a plugin that keeps a minimal set of url params in the url, so it
> can always be copied
> b) use the @jbrowse/react-app package, which does not assume anything
> about the URL, and custom code that feature
>
> -Colin
>
> On Tue, Mar 26, 2024 at 10:07 PM Scott Cain <sc...@sc...> wrote:
>
> Hi Vaneet,
>
> A JBrowse 2 url puts everything in the session into it, so it is *very*
> long. You can get that url from hitting the share link at the top of the
> page and selecting the “long url” option (the short option makes use of a
> url shortener at jbrowse.org) but generally speaking, that long url isn’t
> too useful.
>
> It’s possible to write urls that go into JBrowse 2 that tell it what
> tracks to open and what assembly to use but that gets immediately converted
> to a session.
>
> I hope that helps,
> Scott
>
>
> On Mar 26, 2024, at 2:36 PM, Vaneet Lotay <van...@uc...>
> wrote:
>
> 
>
> Hello all,
>
>
>
> I was just wondering in JBrowse2, is it possible for the URL in my browser
> to dynamically change when I’m selecting different tracks, changing
> location, or even entering different views like the linear synteny view?
> So far it just stays the same once I start from my default session.  It
> would be nice if there’s at least a button that can reveal the true long
> form URL at any point but not sure if that’s possible.  JBrowse 1 had the
> changing URL so that’s why I’m wondering if it’s still accessible somehow.
> This would be a nice feature as it to have as it will make easier to share
> URLs for specific track arrangements with other users.
>
>
>
> Thanks,
>
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Re: [Gmod-ajax] JBrowse2 dynamically changing URL?

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

Thanks guys for the detailed explanation.  So for sessions....isn't that saved local to my browser or is it possible to share it with another user?  If so how long can the session be shared for before it's removed from the server?  Do you have to create a session JSON file to properly store it in the server to make sure it doesn't get deleted before sharing it with someone?

Vaneet
________________________________
From: Colin <col...@gm...>
Sent: March 27, 2024 9:10 AM
To: Scott Cain <sc...@sc...>
Cc: Vaneet Lotay <van...@uc...>; gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse2 dynamically changing URL?

[△EXTERNAL]


Basically what Scott says, but just to add a little more perspective

As a  comparison, JBrowse 1 did have the auto-updating url, and it was a relatively simple system that just stored the current "&loc=chr:1-100" type location that you are viewing in the url. That was pretty much all that was stored...that and tracks and data directory...

With JBrowse 2, we have the ability to have multiple views, and all sorts of  2 just became a kind of complex app with multiple views, and each view can have subviews (think synteny view) and so it became hard to port over the notion of having a simple URL.

I know this is a little unfortunate that the URL bar is not copyable at any time, but as Scott said, we do have the "Share" button that lets you get shareable URL.

If the Share button was undesirable, and someone really wanted live updating URLs they could conceivably....

a) make a plugin that keeps a minimal set of url params in the url, so it can always be copied
b) use the @jbrowse/react-app package, which does not assume anything about the URL, and custom code that feature

-Colin

On Tue, Mar 26, 2024 at 10:07 PM Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Vaneet,

A JBrowse 2 url puts everything in the session into it, so it is *very* long. You can get that url from hitting the share link at the top of the page and selecting the “long url” option (the short option makes use of a url shortener at jbrowse.org<http://jbrowse.org>) but generally speaking, that long url isn’t too useful.

It’s possible to write urls that go into JBrowse 2 that tell it what tracks to open and what assembly to use but that gets immediately converted to a session.

I hope that helps,
Scott


On Mar 26, 2024, at 2:36 PM, Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:



Hello all,



I was just wondering in JBrowse2, is it possible for the URL in my browser to dynamically change when I’m selecting different tracks, changing location, or even entering different views like the linear synteny view?  So far it just stays the same once I start from my default session.  It would be nice if there’s at least a button that can reveal the true long form URL at any point but not sure if that’s possible.  JBrowse 1 had the changing URL so that’s why I’m wondering if it’s still accessible somehow.  This would be a nice feature as it to have as it will make easier to share URLs for specific track arrangements with other users.



Thanks,

Vaneet

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Re: [Gmod-ajax] JBrowse2 dynamically changing URL?

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

Basically what Scott says, but just to add a little more perspective

As a  comparison, JBrowse 1 did have the auto-updating url, and it was a
relatively simple system that just stored the current "&loc=chr:1-100" type
location that you are viewing in the url. That was pretty much all that was
stored...that and tracks and data directory...

With JBrowse 2, we have the ability to have multiple views, and all sorts
of  2 just became a kind of complex app with multiple views, and each view
can have subviews (think synteny view) and so it became hard to port over
the notion of having a simple URL.

I know this is a little unfortunate that the URL bar is not copyable at any
time, but as Scott said, we do have the "Share" button that lets you get
shareable URL.

If the Share button was undesirable, and someone really wanted live
updating URLs they could conceivably....

a) make a plugin that keeps a minimal set of url params in the url, so it
can always be copied
b) use the @jbrowse/react-app package, which does not assume anything about
the URL, and custom code that feature

-Colin

On Tue, Mar 26, 2024 at 10:07 PM Scott Cain <sc...@sc...> wrote:

> Hi Vaneet,
>
> A JBrowse 2 url puts everything in the session into it, so it is *very*
> long. You can get that url from hitting the share link at the top of the
> page and selecting the “long url” option (the short option makes use of a
> url shortener at jbrowse.org) but generally speaking, that long url isn’t
> too useful.
>
> It’s possible to write urls that go into JBrowse 2 that tell it what
> tracks to open and what assembly to use but that gets immediately converted
> to a session.
>
> I hope that helps,
> Scott
>
>
> On Mar 26, 2024, at 2:36 PM, Vaneet Lotay <van...@uc...>
> wrote:
>
> 
>
> Hello all,
>
>
>
> I was just wondering in JBrowse2, is it possible for the URL in my browser
> to dynamically change when I’m selecting different tracks, changing
> location, or even entering different views like the linear synteny view?
> So far it just stays the same once I start from my default session.  It
> would be nice if there’s at least a button that can reveal the true long
> form URL at any point but not sure if that’s possible.  JBrowse 1 had the
> changing URL so that’s why I’m wondering if it’s still accessible somehow.
> This would be a nice feature as it to have as it will make easier to share
> URLs for specific track arrangements with other users.
>
>
>
> Thanks,
>
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] JBrowse2 dynamically changing URL?

[Scott C. <sc...@sc...>]

Hi Vaneet,

A JBrowse 2 url puts everything in the session into it, so it is *very* long. You can get that url from hitting the share link at the top of the page and selecting the “long url” option (the short option makes use of a url shortener at jbrowse.org) but generally speaking, that long url isn’t too useful. 

It’s possible to write urls that go into JBrowse 2 that tell it what tracks to open and what assembly to use but that gets immediately converted to a session. 

I hope that helps,
Scott


> On Mar 26, 2024, at 2:36 PM, Vaneet Lotay <van...@uc...> wrote:
> 
> 
> Hello all,
>  
> I was just wondering in JBrowse2, is it possible for the URL in my browser to dynamically change when I’m selecting different tracks, changing location, or even entering different views like the linear synteny view?  So far it just stays the same once I start from my default session.  It would be nice if there’s at least a button that can reveal the true long form URL at any point but not sure if that’s possible.  JBrowse 1 had the changing URL so that’s why I’m wondering if it’s still accessible somehow.  This would be a nice feature as it to have as it will make easier to share URLs for specific track arrangements with other users.
>  
> Thanks,
> 
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] JBrowse2 dynamically changing URL?

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

Hello all,

I was just wondering in JBrowse2, is it possible for the URL in my browser to dynamically change when I'm selecting different tracks, changing location, or even entering different views like the linear synteny view?  So far it just stays the same once I start from my default session.  It would be nice if there's at least a button that can reveal the true long form URL at any point but not sure if that's possible.  JBrowse 1 had the changing URL so that's why I'm wondering if it's still accessible somehow.  This would be a nice feature as it to have as it will make easier to share URLs for specific track arrangements with other users.

Thanks,

Vaneet

Re: [Gmod-ajax] JBrowse 2 Configuration Options

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

Random extra note:

There is a value called "bicolorPivot" which you can configure to an
absolute value. There is mention of setting bicolorPivotValue to "mean" but
this is unimplemented actually...but is a placeholder for the origin like
JBrowse 1's feature for this...



[image: image.png]


-Colin

On Mon, Mar 18, 2024 at 4:34 PM Colin <col...@gm...> wrote:

> Hi there,
> JBrowse 2 does not have the feature for displaying variance band and
> origin for bigwig tracks
>
> If you wanted to simulate it, you could create a multibigwig track with
> flat lines for the mean and variance bands
>
> I could elaborate on this if interested, but part of the reason why they
> are not implemented is that i worry about presenting potentially misleading
> mean and variance values. The values that are presented by jbrowse 1 are
> actually pretty coarse measurements that are made from summary statistics
> on the global data distribution of the bigwig
>
>
>
> -Colin
>
> On Mon, Mar 18, 2024 at 1:32 PM <aak...@sm...> wrote:
>
>>
>> Hello,
>>
>> I am Master's student from the University of Cologne, currently
>> working on a project to update a web genome browser
>> (https://amaranthgdb.org/popamaranth.html). The first version of this
>> browser uses JBrowse1, where the "origin_color" and "variance_band"
>> options are available for BigWig tracks, as listed in the respective
>> documentation. For the update, I am working with the JBrowse2 desktop
>> app and given my limited experience with JBrowse , I was unable to add
>> the origin line and the variance band to my BigWig tracks. Hence I
>> wanted to reach out and ask if there is a straightforward way of
>> adding these configuration options that I might be missing. If not, I
>> would be grateful if you could provide me with a quick guide on how I
>> can achieve this.
>>
>> Thanks in advance!
>>
>> Aslinur Akturk
>> Institute for Plant Sciences, University of Cologne
>> Biozentrum
>> Zülpicher Str. 47b
>> 50674 Cologne/Germany
>>
>>
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] JBrowse 2 Configuration Options

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

Hi there,
JBrowse 2 does not have the feature for displaying variance band and origin
for bigwig tracks

If you wanted to simulate it, you could create a multibigwig track with
flat lines for the mean and variance bands

I could elaborate on this if interested, but part of the reason why they
are not implemented is that i worry about presenting potentially misleading
mean and variance values. The values that are presented by jbrowse 1 are
actually pretty coarse measurements that are made from summary statistics
on the global data distribution of the bigwig



-Colin

On Mon, Mar 18, 2024 at 1:32 PM <aak...@sm...> wrote:

>
> Hello,
>
> I am Master's student from the University of Cologne, currently
> working on a project to update a web genome browser
> (https://amaranthgdb.org/popamaranth.html). The first version of this
> browser uses JBrowse1, where the "origin_color" and "variance_band"
> options are available for BigWig tracks, as listed in the respective
> documentation. For the update, I am working with the JBrowse2 desktop
> app and given my limited experience with JBrowse , I was unable to add
> the origin line and the variance band to my BigWig tracks. Hence I
> wanted to reach out and ask if there is a straightforward way of
> adding these configuration options that I might be missing. If not, I
> would be grateful if you could provide me with a quick guide on how I
> can achieve this.
>
> Thanks in advance!
>
> Aslinur Akturk
> Institute for Plant Sciences, University of Cologne
> Biozentrum
> Zülpicher Str. 47b
> 50674 Cologne/Germany
>
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse 2 Configuration Options

[<aak...@sm...>]

Hello,

I am Master's student from the University of Cologne, currently  
working on a project to update a web genome browser  
(https://amaranthgdb.org/popamaranth.html). The first version of this  
browser uses JBrowse1, where the "origin_color" and "variance_band"  
options are available for BigWig tracks, as listed in the respective  
documentation. For the update, I am working with the JBrowse2 desktop  
app and given my limited experience with JBrowse , I was unable to add  
the origin line and the variance band to my BigWig tracks. Hence I  
wanted to reach out and ask if there is a straightforward way of  
adding these configuration options that I might be missing. If not, I  
would be grateful if you could provide me with a quick guide on how I  
can achieve this.

Thanks in advance!

Aslinur Akturk
Institute for Plant Sciences, University of Cologne
Biozentrum
Zülpicher Str. 47b
50674 Cologne/Germany

Re: [Gmod-ajax] Running Apollo in JBrowse

[Dorita A. <dor...@um...>]

Dear Colin,

I thank you for clearing this issue for me. I will read a bit more about
'running a web server'.
In the meantime can you please advice me on which application to use for a
small amount of manual annotation curation of a relatively small genome
(150kbp) on a Mac?

Yours truly,
Dorita Agius B.Sc. M.Phil.
Senior Lecturer II
RM D004 Junior College
University of Malta
Phone: 00356 7938 2887
dor...@um...



On Thu, 29 Feb 2024 at 23:43, Colin <col...@gm...> wrote:

> Hi Dorita
>
> Apollo is a server side app, written in java, that basically has it's own
> installation instructions here
> https://genomearchitect.readthedocs.io/en/latest/
>
> It requires running a server, so it doens't work with JBrowse desktop, you
> would need to run a web server to set it up.
>
> The current Apollo ("Apollo v2") also only works with JBrowse 1 now, but
> we are working on a new version of Apollo ("Apollo v3") that is compatible
> with JBrowse 2
>
> Hope that helps!
> -Colin
>
>
>
> On Thu, Feb 29, 2024 at 2:52 PM Dorita Agius <dor...@um...>
> wrote:
>
>> Dear Sir or Madame,
>>
>> I am trying to run Apollo within JBrowse on desktop (MacBook Pro).
>> However in both JBrowse V2.10.2 and 1.16.11 and in both cases I cannot find
>> the plugin store for installation of Apollo.
>> What am I doing wrong please?
>>
>> If this is not the right email address to use for this difficulty can you
>> guide me to the right one please?
>>
>> [image: image.png]
>>
>>
>>
>> [image: image.png]
>>
>> Thank you
>>
>> Yours truly
>>
>> Dorita Agius B.Sc. M.Phil.
>> Senior Lecturer II
>> RM D004 Junior College
>> University of Malta
>> Phone: 00356 7938 2887
>> dor...@um...
>>
>>
>> *The contents of this email are subject to these terms
>> <https://www.um.edu.mt/disclaimer/email/>.*
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

-- 
*The contents of this email are subject to *these terms 
<https://www.um.edu.mt/disclaimer/email/>.**

Re: [Gmod-ajax] Running Apollo in JBrowse

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

Hi Dorita

Apollo is a server side app, written in java, that basically has it's own
installation instructions here
https://genomearchitect.readthedocs.io/en/latest/

It requires running a server, so it doens't work with JBrowse desktop, you
would need to run a web server to set it up.

The current Apollo ("Apollo v2") also only works with JBrowse 1 now, but we
are working on a new version of Apollo ("Apollo v3") that is compatible
with JBrowse 2

Hope that helps!
-Colin



On Thu, Feb 29, 2024 at 2:52 PM Dorita Agius <dor...@um...> wrote:

> Dear Sir or Madame,
>
> I am trying to run Apollo within JBrowse on desktop (MacBook Pro). However
> in both JBrowse V2.10.2 and 1.16.11 and in both cases I cannot find the
> plugin store for installation of Apollo.
> What am I doing wrong please?
>
> If this is not the right email address to use for this difficulty can you
> guide me to the right one please?
>
> [image: image.png]
>
>
>
> [image: image.png]
>
> Thank you
>
> Yours truly
>
> Dorita Agius B.Sc. M.Phil.
> Senior Lecturer II
> RM D004 Junior College
> University of Malta
> Phone: 00356 7938 2887
> dor...@um...
>
>
> *The contents of this email are subject to these terms
> <https://www.um.edu.mt/disclaimer/email/>.*
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Running Apollo in JBrowse

[Dorita A. <dor...@um...>]

Dear Sir or Madame,

I am trying to run Apollo within JBrowse on desktop (MacBook Pro). However
in both JBrowse V2.10.2 and 1.16.11 and in both cases I cannot find the
plugin store for installation of Apollo.
What am I doing wrong please?

If this is not the right email address to use for this difficulty can you
guide me to the right one please?

[image: image.png]



[image: image.png]

Thank you

Yours truly

Dorita Agius B.Sc. M.Phil.
Senior Lecturer II
RM D004 Junior College
University of Malta
Phone: 00356 7938 2887
dor...@um...

-- 
*The contents of this email are subject to *these terms 
<https://www.um.edu.mt/disclaimer/email/>.**

Re: [Gmod-ajax] Requirements for a GFF3 to render properly?

[Hans Vasquez-G. <hva...@un...>]

Hi Scott,

Thank you! I converted the file from GTF to GFF with agat utility. Now the tracks are properly rendering.

Betss,
-Hans
________________________________
From: Scott Cain <sc...@sc...>
Sent: Thursday, January 11, 2024 3:01 PM
To: Hans Vasquez-Gross <hva...@un...>
Cc: gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] Requirements for a GFF3 to render properly?


[EXTERNAL EMAIL]

Another thing I should have mentioned when I said this looked like GTF: GTF is frequently called GFF2.5. What you posted would also pass as GFF 2.

On Thu, Jan 11, 2024 at 2:45 PM Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote:
Hi Hans,

I'd say the problem is primarily that the snippet you've shown isn't GFF3; it looks much more like GTF (GFF3 would have "tag=value;tag2=value2" in the ninth column, as opposed to 'tag "value"; tag2 "value2"' in the ninth column). While JBrowse 2 does support GTF, it has some drawbacks, the biggest of which is there isn't an indexed form of it, so the tracks will load very slowly since JBrowse has to load the entire file and parse it in order to draw any portion of it. If you had GFF3, each of the exon features would have a "Parent" tag that pointed to the ID of the parent transcript.

The other thing that jumps out at me for the data snippet you provided is that all of the transcripts appear to share the same start and end coordinates of the child exons, so they would only show up as individual exons anyway. I would guess that elsewhere in your GTF file you have more complicated examples with transcripts that have multiple exon children.

So, it's hard to say what I would expect to see without a better example of your GTF, but you probably want to look at generated GFF3 anyway, so that you can take advantage of tabix indexing of the GFF3 files.

Of course, feel free to follow up with more questions or example data and we can figure out where to go from there.

Scott


On Thu, Jan 11, 2024 at 2:29 PM Hans Vasquez-Gross <hva...@un...<mailto:hva...@un...>> wrote:
Hello All,

I have the output from isoseq collapse then pigeon index to create a sorted .gff3 file for a new assembly. Currently, this gff3 file has transcript and exon definitions.  However, when I load this track data on JBrowse2, it shows the transcripts as one large unit and the exons as a separate unit. It doesn't seem to correct render the intron/exon boundaries. The annotation track is on top in yellow and the isoseq_reads bam file is below.

Example data:
##pacbio-collapse-version 1.0
##date Thu Jan 11 00:10:30 2024 UTC
ctg_p_c_003493_0_75000_89999  PacBio      transcript  11587 12122 .     -     .     gene_id "PB.32086"; transcript_id "PB.32086.1";
ctg_p_c_003493_0_75000_89999  PacBio      exon  11587 12122 .     -     .     gene_id "PB.32086"; transcript_id "PB.32086.1";
ctg_p_c_033075_0  PacBio      transcript  20564 22031 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.1";
ctg_p_c_033075_0  PacBio      exon  20564 22031 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.1";
ctg_p_c_033075_0  PacBio      transcript  20564 21887 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.2";
ctg_p_c_033075_0  PacBio      exon  20564 21887 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.2";
ctg_p_c_033075_0  PacBio      transcript  20564 21758 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.3";
ctg_p_c_033075_0  PacBio      exon  20564 21758 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.3";


Any suggestions?

Thank you,
-Hans


--



[signature_998258195]

Hans Vasquez-Gross, Ph.D

Bioinformatics Scientist,
Nevada Bioinformatics Center

https://www.unr.edu/bioinformatics

hva...@un...<mailto:hva...@un...>

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GMOD Project Manager (http://gmod.org/)                            216-392-3087
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Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott at scottcain dot net
GMOD Project Manager (http://gmod.org/)                            216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (https://hcmi-searchable-catalog.nci.nih.gov/)

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Re: [Gmod-ajax] Requirements for a GFF3 to render properly?

[Scott C. <sc...@sc...>]

Hi Hans,

I'd say the problem is primarily that the snippet you've shown isn't GFF3;
it looks much more like GTF (GFF3 would have "tag=value;tag2=value2" in the
ninth column, as opposed to 'tag "value"; tag2 "value2"' in the ninth
column). While JBrowse 2 does support GTF, it has some drawbacks, the
biggest of which is there isn't an indexed form of it, so the tracks will
load very slowly since JBrowse has to load the entire file and parse it in
order to draw any portion of it. If you had GFF3, each of the exon features
would have a "Parent" tag that pointed to the ID of the parent transcript.

The other thing that jumps out at me for the data snippet you provided is
that all of the transcripts appear to share the same start and end
coordinates of the child exons, so they would only show up as individual
exons anyway. I would guess that elsewhere in your GTF file you have more
complicated examples with transcripts that have multiple exon children.

So, it's hard to say what I would expect to see without a better example of
your GTF, but you probably want to look at generated GFF3 anyway, so that
you can take advantage of tabix indexing of the GFF3 files.

Of course, feel free to follow up with more questions or example data and
we can figure out where to go from there.

Scott


On Thu, Jan 11, 2024 at 2:29 PM Hans Vasquez-Gross <hva...@un...>
wrote:

> Hello All,
>
> I have the output from isoseq collapse then pigeon index to create a
> sorted .gff3 file for a new assembly. Currently, this gff3 file has
> transcript and exon definitions.  However, when I load this track data on
> JBrowse2, it shows the transcripts as one large unit and the exons as a
> separate unit. It doesn't seem to correct render the intron/exon
> boundaries. The annotation track is on top in yellow and the isoseq_reads
> bam file is below.
>
> Example data:
> ##pacbio-collapse-version 1.0
> ##date Thu Jan 11 00:10:30 2024 UTC
> ctg_p_c_003493_0_75000_89999 PacBio transcript 11587 12122 . - . gene_id
> "PB.32086"; transcript_id "PB.32086.1";
> ctg_p_c_003493_0_75000_89999 PacBio exon 11587 12122 . - . gene_id
> "PB.32086"; transcript_id "PB.32086.1";
> ctg_p_c_033075_0 PacBio transcript 20564 22031 . + . gene_id "PB.31043";
> transcript_id "PB.31043.1";
> ctg_p_c_033075_0 PacBio exon 20564 22031 . + . gene_id "PB.31043";
> transcript_id "PB.31043.1";
> ctg_p_c_033075_0 PacBio transcript 20564 21887 . + . gene_id "PB.31043";
> transcript_id "PB.31043.2";
> ctg_p_c_033075_0 PacBio exon 20564 21887 . + . gene_id "PB.31043";
> transcript_id "PB.31043.2";
> ctg_p_c_033075_0 PacBio transcript 20564 21758 . + . gene_id "PB.31043";
> transcript_id "PB.31043.3";
> ctg_p_c_033075_0 PacBio exon 20564 21758 . + . gene_id "PB.31043";
> transcript_id "PB.31043.3";
>
>
> Any suggestions?
>
> Thank you,
> -Hans
>
> --
>
>
>
> [image: signature_998258195]
>
> *Hans Vasquez-Gross, Ph.D*
>
> Bioinformatics Scientist,
> Nevada Bioinformatics Center
>
> https://www.unr.edu/bioinformatics
>
> hva...@un...
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)

Re: [Gmod-ajax] Requirements for a GFF3 to render properly?

[Scott C. <sc...@sc...>]

Another thing I should have mentioned when I said this looked like GTF: GTF
is frequently called GFF2.5. What you posted would also pass as GFF 2.

On Thu, Jan 11, 2024 at 2:45 PM Scott Cain <sc...@sc...> wrote:

> Hi Hans,
>
> I'd say the problem is primarily that the snippet you've shown isn't GFF3;
> it looks much more like GTF (GFF3 would have "tag=value;tag2=value2" in the
> ninth column, as opposed to 'tag "value"; tag2 "value2"' in the ninth
> column). While JBrowse 2 does support GTF, it has some drawbacks, the
> biggest of which is there isn't an indexed form of it, so the tracks will
> load very slowly since JBrowse has to load the entire file and parse it in
> order to draw any portion of it. If you had GFF3, each of the exon features
> would have a "Parent" tag that pointed to the ID of the parent transcript.
>
> The other thing that jumps out at me for the data snippet you provided is
> that all of the transcripts appear to share the same start and end
> coordinates of the child exons, so they would only show up as individual
> exons anyway. I would guess that elsewhere in your GTF file you have more
> complicated examples with transcripts that have multiple exon children.
>
> So, it's hard to say what I would expect to see without a better example
> of your GTF, but you probably want to look at generated GFF3 anyway, so
> that you can take advantage of tabix indexing of the GFF3 files.
>
> Of course, feel free to follow up with more questions or example data and
> we can figure out where to go from there.
>
> Scott
>
>
> On Thu, Jan 11, 2024 at 2:29 PM Hans Vasquez-Gross <hva...@un...>
> wrote:
>
>> Hello All,
>>
>> I have the output from isoseq collapse then pigeon index to create a
>> sorted .gff3 file for a new assembly. Currently, this gff3 file has
>> transcript and exon definitions.  However, when I load this track data on
>> JBrowse2, it shows the transcripts as one large unit and the exons as a
>> separate unit. It doesn't seem to correct render the intron/exon
>> boundaries. The annotation track is on top in yellow and the isoseq_reads
>> bam file is below.
>>
>> Example data:
>> ##pacbio-collapse-version 1.0
>> ##date Thu Jan 11 00:10:30 2024 UTC
>> ctg_p_c_003493_0_75000_89999 PacBio transcript 11587 12122 . - . gene_id
>> "PB.32086"; transcript_id "PB.32086.1";
>> ctg_p_c_003493_0_75000_89999 PacBio exon 11587 12122 . - . gene_id
>> "PB.32086"; transcript_id "PB.32086.1";
>> ctg_p_c_033075_0 PacBio transcript 20564 22031 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.1";
>> ctg_p_c_033075_0 PacBio exon 20564 22031 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.1";
>> ctg_p_c_033075_0 PacBio transcript 20564 21887 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.2";
>> ctg_p_c_033075_0 PacBio exon 20564 21887 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.2";
>> ctg_p_c_033075_0 PacBio transcript 20564 21758 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.3";
>> ctg_p_c_033075_0 PacBio exon 20564 21758 . + . gene_id "PB.31043";
>> transcript_id "PB.31043.3";
>>
>>
>> Any suggestions?
>>
>> Thank you,
>> -Hans
>>
>> --
>>
>>
>>
>> [image: signature_998258195]
>>
>> *Hans Vasquez-Gross, Ph.D*
>>
>> Bioinformatics Scientist,
>> Nevada Bioinformatics Center
>>
>> https://www.unr.edu/bioinformatics
>>
>> hva...@un...
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                                  scott
> at scottcain dot net
> GMOD Project Manager (http://gmod.org/)
> 216-392-3087
> WormBase Developer (http://wormbase.org/)
> Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
> VirusSeq Project Manager (https://virusseq-dataportal.ca/)
> Human Cancer Models Initiative Project Manager (
> https://hcmi-searchable-catalog.nci.nih.gov/)
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                                  scott
at scottcain dot net
GMOD Project Manager (http://gmod.org/)
216-392-3087
WormBase Developer (http://wormbase.org/)
Alliance of Genome Resources Group Leader (http://alliancegenome.org/)
VirusSeq Project Manager (https://virusseq-dataportal.ca/)
Human Cancer Models Initiative Project Manager (
https://hcmi-searchable-catalog.nci.nih.gov/)

[Gmod-ajax] Requirements for a GFF3 to render properly?

[Hans Vasquez-G. <hva...@un...>]

Hello All,

I have the output from isoseq collapse then pigeon index to create a sorted .gff3 file for a new assembly. Currently, this gff3 file has transcript and exon definitions.  However, when I load this track data on JBrowse2, it shows the transcripts as one large unit and the exons as a separate unit. It doesn't seem to correct render the intron/exon boundaries. The annotation track is on top in yellow and the isoseq_reads bam file is below.

Example data:
##pacbio-collapse-version 1.0
##date Thu Jan 11 00:10:30 2024 UTC
ctg_p_c_003493_0_75000_89999  PacBio      transcript  11587 12122 .     -     .     gene_id "PB.32086"; transcript_id "PB.32086.1";
ctg_p_c_003493_0_75000_89999  PacBio      exon  11587 12122 .     -     .     gene_id "PB.32086"; transcript_id "PB.32086.1";
ctg_p_c_033075_0  PacBio      transcript  20564 22031 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.1";
ctg_p_c_033075_0  PacBio      exon  20564 22031 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.1";
ctg_p_c_033075_0  PacBio      transcript  20564 21887 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.2";
ctg_p_c_033075_0  PacBio      exon  20564 21887 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.2";
ctg_p_c_033075_0  PacBio      transcript  20564 21758 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.3";
ctg_p_c_033075_0  PacBio      exon  20564 21758 .     +     .     gene_id "PB.31043"; transcript_id "PB.31043.3";


Any suggestions?

Thank you,
-Hans


--



[signature_998258195]

Hans Vasquez-Gross, Ph.D

Bioinformatics Scientist,
Nevada Bioinformatics Center

https://www.unr.edu/bioinformatics

hva...@un...<mailto:hva...@un...>

Re: [Gmod-ajax] text-index problem

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

Hi,

After upgrading Node.js to 20, the index function is fully restored (tested
with various options).

Thanks for the help from the developers!

Ke

On Wed, Dec 6, 2023 at 10:14 PM Ke Jiang <bio...@gm...> wrote:

> Thanks, Colin! I’ll give upgrading node.js a try and report back how it
> works.
>
> On Wed, Dec 6, 2023 at 6:12 PM Colin <col...@gm...> wrote:
>
>> Sorry there was a typo in the last email, I meant to say node 14 and 16
>> are end of life, 18 is not, so upgrading to 18 or 20 is safe (those are the
>> current "LTS" versions)
>>
>> -Colin
>>
>> On Wed, Dec 6, 2023 at 7:11 PM Colin <col...@gm...> wrote:
>>
>>> Hi there,
>>> It looks like replaceAll was added in nodejs 15. If you run node
>>> --version you can check which version you have. I would imagine that
>>> upgrading could help if e.g. you are node 14 (both node 16 and node 18 are
>>> now officially "end of life" so it is good to stay updated if possible)
>>>
>>> We can probably do a better job in our CLI trying to report errors with
>>> this. We can maybe also even consider trying to support older node or at
>>> least not using bleeding edge features all the time, as I know it is kind
>>> of tricky to stay updated
>>>
>>> -Colin
>>>
>>> On Wed, Dec 6, 2023 at 3:52 PM Ke Jiang <bio...@gm...> wrote:
>>>
>>>> Hi,
>>>>
>>>> I tried to rebuild some indice with new tracks added, but experienced
>>>> the following error message:
>>>>
>>>> UnhandledPromiseRejectionWarning: TypeError:
>>>> JSON.stringify(...).replaceAll is not a function
>>>>
>>>> Even after cleaning up the old indice JSON chunk, I keep having this
>>>> error with "text-index" with all new tracks. Based on some searches, it
>>>> looks like this is caused by an older version of node.js. Does anyone have
>>>> similar problems? If so, does upgrading the node.js solve it? I'm on
>>>> JBrowse2 2.8.0.
>>>>
>>>> Thanks!
>>>>
>>>> Ke
>>>>
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>

Re: [Gmod-ajax] JBrowse URL params: specify height

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

Currently, the url params don't allow specifying height, but that is a good
idea, to provide various parameters. However you can pre-configure the
height of the track in the config.json as an alternative

Example of pre-configuring height on a track with height on the display

  {
      "type": "FeatureTrack",
      "trackId": "mygenes",
      "assemblyNames": ["hg19"],
      "name": "genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": { "uri": "volvox.sort.gff3.gz" },
        "index": { "location": {"uri": "volvox.sort.gff3.gz.tbi" } }
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "height": 600,
          "displayId": "mygenes_LinearBasicDisplay"
        }
      ]
    }



Also, we may look into auto-adjusting the track height to the contents of
the track or something of that sort
https://github.com/GMOD/jbrowse-components/issues/534


-Colin

On Wed, Dec 20, 2023 at 4:58 PM Vaneet Lotay <van...@uc...>
wrote:

> Hi all,
>
>
>
> I was looking at this doc page for JBrowse2:
>
>
>
> https://jbrowse.org/jb2/docs/urlparams/
>
>
>
> I was just wondering is there a way to specify additional parameters via
> URL besides the 5 that were mentioned?  Specifically, I’m thinking of track
> height, since when I tried using some specific parameters in the URL to go
> to the position of a gene model, the track height wasn’t long enough to
> cover all the transcripts in the gene model, it was cut off.
>
>
>
> Thanks,
>
>
> Vaneet
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>