gmod-ajax — JBrowse list

Re: [Gmod-ajax] Collapsing categories

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

Well currently you can collapse parent category as well as all subcategories if you specify each subcategory and parent category in the ‘collapsedCategories’ field.  I was looking for a shortcut to collapse all subcategories under a parent subcategory with maybe a wildcard character or some alternative that would work in your development.  It would be great if something to this effect could be added in a future release, because I am working with a lot of nested subcategories sometimes across 3-4 levels.  Essentially having a collapse all function from a higher level in the configuration would be nice.

Thanks,

Vaneet

From: Colin <col...@gm...>
Sent: Monday, September 28, 2020 4:33 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: [Gmod-ajax] Collapsing categories

[△EXTERNAL]

That is interesting. I don't think anything like this exists. I guess currently the idea would be to collapse the parent category. rather than collapse all subcategories, but I guess if there is a mix of tracks and categories at one level you want to collapse all the categories at that level rather than the parent?

-Colin

On Mon, Sep 28, 2020 at 1:27 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I was wondering is there a way to collapse subcategories within a main category without having to specify every single subcategory separately within this field:

trackSelector→collapsedCategories

If not, it would be nice for this feature to be added to JBrowse somehow using a special wildcard character like perhaps this for example:

collapsedCategories : “Category1/*,Category2/Subcategory1/*’

If it’s not a feature please let me know if I should add a request to GitHub, as I think it would be very helpful when dealing with a lot of categories and subcategories which is the case in my scenario.

Thanks,

Vaneet

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

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

Re: [Gmod-ajax] Jbrowse track selector integration within another UI

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

Hi there,

Generally it might be difficult to control the tracklist super dynamically,
you can use both publish and subscribe, see docs (this is one of the more
messy doc pages unfortunately :))

https://jbrowse.org/docs/events.html

See the example on adding a track using publish at the moment, and note how
it has to go through some extra hoops to use JBrowse.addStoreConfig before
doing the publish with the /jbrowse/v1/v/tracks/replace  (the replace event
creates new track if none exists)
Let me know if that helps

-Colin

On Mon, Sep 28, 2020 at 1:39 PM Scott Cain <sc...@sc...> wrote:

> Hi Tom,
>
> I'm going to forward this to the JBrowse mailing list.
>
> Scott
>
>
> On Mon, Sep 28, 2020 at 7:21 AM Shorter, Tom <ts...@le...>
> wrote:
>
>> Good afternoon,
>>
>> We have a webpage which displays a lot of meta data about studies and
>> their experiments and from there we allow the users to display the
>> information on a genome browser based on any tracks they have selected in
>> any of the previous screens.
>>
>> I would like to move to using Jbrowse but the main hurdle is the track
>> selector functionality, I cannot seem to find an easy way of connecting the
>> tracks selected on other parts of the website up to the browser interface.
>> Specifically, I want the track selector to only display the tracks selected
>> in other areas of the webpage, and not all available tracks as is the
>> default.
>>
>> I am able to update the URL to render the desired tracks and I could
>> build a custom track selector to only view the tracks I want but this then
>> requires a page refresh to view the changes whereas I want to keep the
>> dynamic track selections so I don't want to use this method.
>>
>> It is possible to navigate through our site without any page refreshes
>> occurring, with some changes being made, so the browser would not be
>> refreshed/reloaded unless specifically told to do so. I believe this should
>> be possible to do but I'm not sure how to connect my track select
>> checkboxes up with Jbrowse.
>>
>> I believe it is the below lines of code which allow this functionality
>> within the track selector :
>>
>>       this.browser.subscribe( '/jbrowse/v1/c/tracks/show',
>>                        lang.hitch( this, 'setTracksActive' ));
>>        // subscribe to commands coming from the the controller
>>        this.browser.subscribe( '/jbrowse/v1/c/tracks/hide',
>>                        lang.hitch( this, 'setTracksInactive' ));
>>        this.browser.subscribe( '/jbrowse/v1/c/tracks/delete',
>>                        lang.hitch( this, 'setTracksInactive' ));
>>
>> Are there any more functions I could call with my sections which would
>> produce the same behaviour and allow me to show/hide the tracks
>> dynamically? I haven't been able to find a function which toggles if the
>> track is shown or hidden and if one does exist then that should be all I
>> need to use. Alternatively, if there is a function which would allow me to
>> turn on certain tracks
>>
>> many thanks,
>>
>> Tom Shorter
>>
>> Research Assistant
>>
>> Department of Genetics and Genome Biology
>> University of Leicester
>> University Road
>> Leicester, LE1 7RH, UK
>>
>> ts...@le...
>>
>>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Collapsing categories

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

That is interesting. I don't think anything like this exists. I guess
currently the idea would be to collapse the parent category. rather than
collapse all subcategories, but I guess if there is a mix of tracks and
categories at one level you want to collapse all the categories at that
level rather than the parent?

-Colin

On Mon, Sep 28, 2020 at 1:27 PM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
>
>
> I was wondering is there a way to collapse subcategories within a main
> category without having to specify every single subcategory separately
> within this field:
>
>
>
> trackSelector→collapsedCategories
>
>
>
> If not, it would be nice for this feature to be added to JBrowse somehow
> using a special wildcard character like perhaps this for example:
>
>
>
> collapsedCategories : “Category1/*,Category2/Subcategory1/*’
>
>
>
> If it’s not a feature please let me know if I should add a request to
> GitHub, as I think it would be very helpful when dealing with a lot of
> categories and subcategories which is the case in my scenario.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building – University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Jbrowse track selector integration within another UI

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

Hi Tom,

I'm going to forward this to the JBrowse mailing list.

Scott


On Mon, Sep 28, 2020 at 7:21 AM Shorter, Tom <ts...@le...> wrote:

> Good afternoon,
>
> We have a webpage which displays a lot of meta data about studies and
> their experiments and from there we allow the users to display the
> information on a genome browser based on any tracks they have selected in
> any of the previous screens.
>
> I would like to move to using Jbrowse but the main hurdle is the track
> selector functionality, I cannot seem to find an easy way of connecting the
> tracks selected on other parts of the website up to the browser interface.
> Specifically, I want the track selector to only display the tracks selected
> in other areas of the webpage, and not all available tracks as is the
> default.
>
> I am able to update the URL to render the desired tracks and I could build
> a custom track selector to only view the tracks I want but this then
> requires a page refresh to view the changes whereas I want to keep the
> dynamic track selections so I don't want to use this method.
>
> It is possible to navigate through our site without any page refreshes
> occurring, with some changes being made, so the browser would not be
> refreshed/reloaded unless specifically told to do so. I believe this should
> be possible to do but I'm not sure how to connect my track select
> checkboxes up with Jbrowse.
>
> I believe it is the below lines of code which allow this functionality
> within the track selector :
>
>       this.browser.subscribe( '/jbrowse/v1/c/tracks/show',
>                        lang.hitch( this, 'setTracksActive' ));
>        // subscribe to commands coming from the the controller
>        this.browser.subscribe( '/jbrowse/v1/c/tracks/hide',
>                        lang.hitch( this, 'setTracksInactive' ));
>        this.browser.subscribe( '/jbrowse/v1/c/tracks/delete',
>                        lang.hitch( this, 'setTracksInactive' ));
>
> Are there any more functions I could call with my sections which would
> produce the same behaviour and allow me to show/hide the tracks
> dynamically? I haven't been able to find a function which toggles if the
> track is shown or hidden and if one does exist then that should be all I
> need to use. Alternatively, if there is a function which would allow me to
> turn on certain tracks
>
> many thanks,
>
> Tom Shorter
>
> Research Assistant
>
> Department of Genetics and Genome Biology
> University of Leicester
> University Road
> Leicester, LE1 7RH, UK
>
> ts...@le...
>
>

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] Collapsing categories

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

Hello,

I was wondering is there a way to collapse subcategories within a main category without having to specify every single subcategory separately within this field:

trackSelector→collapsedCategories

If not, it would be nice for this feature to be added to JBrowse somehow using a special wildcard character like perhaps this for example:

collapsedCategories : “Category1/*,Category2/Subcategory1/*’

If it’s not a feature please let me know if I should add a request to GitHub, as I think it would be very helpful when dealing with a lot of categories and subcategories which is the case in my scenario.

Thanks,

Vaneet

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

Re: [Gmod-ajax] Problem with BAM .csi index file

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

You will need JBrowse 1.16.10 to use replaceRefRename but if you have this
you add this to your jbrowse.conf

replaceRefRename = function(ref) { return
ref.toLowerCase().replace('chr','') }

Also went ahead and updated the docs with an example for both of those,
will be on website soon

-Colin



On Thu, Sep 24, 2020 at 8:03 PM JM C <jua...@gm...> wrote:

> MG I must have been using the new version in igv. Thanks guys. I see these
> two options:
> customRefRename and replaceRefRename, but I'm not sure according to the
> doc, what to set in those. Thanks again
> --
> *Juan Manuel Crescente*
>
> This message is confidential. You may not copy this message or disclose
> its contents to anyone.
> Please consider the environment before printing this email.
>
>
> On Thu, Sep 24, 2020 at 8:57 PM Colin <col...@gm...> wrote:
>
>> Note also, JBrowse could be programmed to support this out of the box
>> without a custom configuration, we are just trying to help find a solution
>> that works for you, with what we have now :)
>>
>> To see jbrowse's current capabilities for this see
>> https://github.com/GMOD/jbrowse/blob/master/tests/js_tests/spec/RegularizeRefSeqs.spec.js
>>
>> The chr2A/2A does not work but we could add that to our test matrix, etc
>>
>> -Colin
>>
>> On Thu, Sep 24, 2020 at 7:25 PM Colin <col...@gm...> wrote:
>>
>>> While it's nice igv loads it, but they are likely doing similar
>>> "smoothing over" the differences in refname between your bam and the
>>> reference genome.
>>>
>>> Most programs do not do any of this smoothing over of this and so it is
>>> generally better to ensure your data is using the same reference sequence
>>> names
>>>
>>> Try:
>>>
>>> samtools view
>>> http://165.227.95.85/jbrowse/data/Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam
>>> 2A
>>>
>>> This fails because your BAM file uses chr2A not 2A.
>>>
>>> As noted above, jbrowse can also try to help this case too, but requires
>>> the replaceRefRename callback
>>>
>>> -Colin
>>>
>>> On Thu, Sep 24, 2020 at 7:03 PM JM C <jua...@gm...> wrote:
>>>
>>>> HI Scott
>>>>
>>>> thank you for your reply. I see your point in there. This shouldn't be
>>>> the case since I'm using the same genome with the same bam file in igv and
>>>> it's working correctly.
>>>>
>>>> This is my track config btw
>>>>
>>>> [ tracks.bam_biointa_2002 ]
>>>> storeClass=JBrowse/Store/SeqFeature/BAM
>>>>
>>>> urlTemplate=Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam
>>>> category=BAM
>>>> type=Alignments2
>>>> key=Biointa 2002
>>>>
>>>> csiUrlTemplate=Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam.csi
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> *Juan Manuel Crescente*
>>>>
>>>> This message is confidential. You may not copy this message or disclose
>>>> its contents to anyone.
>>>> Please consider the environment before printing this email.
>>>>
>>>>
>>>> On Thu, Sep 24, 2020 at 7:10 PM Scott Cain <sc...@sc...> wrote:
>>>>
>>>>> Hi Juan,
>>>>>
>>>>> Almost always, when this happens, it's because the name of the
>>>>> reference sequence in the BAM file is different from the names of the
>>>>> reference sequences in the seq/refSeqs.json file.  If that's the case and
>>>>> you have the very fresh 1.16.10 release, you can use the
>>>>> customRefRename and replaceRefRename  options described here:
>>>>> https://jbrowse.org/docs/global_options.html.  If you need to go down
>>>>> that path, and enlightenment doesn't immediately strike you, please feel
>>>>> free to write back to this list.
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Thu, Sep 24, 2020 at 2:56 PM JM C <jua...@gm...> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I'm setting up a demo jbrowse with a bam file with .csi index.
>>>>>>
>>>>>>
>>>>>> http://165.227.95.85/jbrowse/?loc=2A%3A651960001..674020000&tracks=b19&highlight=
>>>>>>
>>>>>> I can see the track and got no errors but the track is empty in the
>>>>>> browser. Not sure how to troubleshoot this, any suggestions?
>>>>>>
>>>>>>
>>>>>> --
>>>>>> *Juan Manuel Crescente*
>>>>>>
>>>>>> This message is confidential. You may not copy this message or
>>>>>> disclose its contents to anyone.
>>>>>> Please consider the environment before printing this email.
>>>>>> _______________________________________________
>>>>>> Gmod-ajax mailing list
>>>>>> Gmo...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at
>>>>> scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>>>
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>

Re: [Gmod-ajax] Problem with BAM .csi index file

[JM C <jua...@gm...>]

MG I must have been using the new version in igv. Thanks guys. I see these
two options:
customRefRename and replaceRefRename, but I'm not sure according to the
doc, what to set in those. Thanks again
--
*Juan Manuel Crescente*

This message is confidential. You may not copy this message or disclose its
contents to anyone.
Please consider the environment before printing this email.


On Thu, Sep 24, 2020 at 8:57 PM Colin <col...@gm...> wrote:

> Note also, JBrowse could be programmed to support this out of the box
> without a custom configuration, we are just trying to help find a solution
> that works for you, with what we have now :)
>
> To see jbrowse's current capabilities for this see
> https://github.com/GMOD/jbrowse/blob/master/tests/js_tests/spec/RegularizeRefSeqs.spec.js
>
> The chr2A/2A does not work but we could add that to our test matrix, etc
>
> -Colin
>
> On Thu, Sep 24, 2020 at 7:25 PM Colin <col...@gm...> wrote:
>
>> While it's nice igv loads it, but they are likely doing similar
>> "smoothing over" the differences in refname between your bam and the
>> reference genome.
>>
>> Most programs do not do any of this smoothing over of this and so it is
>> generally better to ensure your data is using the same reference sequence
>> names
>>
>> Try:
>>
>> samtools view
>> http://165.227.95.85/jbrowse/data/Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam
>> 2A
>>
>> This fails because your BAM file uses chr2A not 2A.
>>
>> As noted above, jbrowse can also try to help this case too, but requires
>> the replaceRefRename callback
>>
>> -Colin
>>
>> On Thu, Sep 24, 2020 at 7:03 PM JM C <jua...@gm...> wrote:
>>
>>> HI Scott
>>>
>>> thank you for your reply. I see your point in there. This shouldn't be
>>> the case since I'm using the same genome with the same bam file in igv and
>>> it's working correctly.
>>>
>>> This is my track config btw
>>>
>>> [ tracks.bam_biointa_2002 ]
>>> storeClass=JBrowse/Store/SeqFeature/BAM
>>>
>>> urlTemplate=Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam
>>> category=BAM
>>> type=Alignments2
>>> key=Biointa 2002
>>>
>>> csiUrlTemplate=Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam.csi
>>>
>>>
>>>
>>>
>>> --
>>> *Juan Manuel Crescente*
>>>
>>> This message is confidential. You may not copy this message or disclose
>>> its contents to anyone.
>>> Please consider the environment before printing this email.
>>>
>>>
>>> On Thu, Sep 24, 2020 at 7:10 PM Scott Cain <sc...@sc...> wrote:
>>>
>>>> Hi Juan,
>>>>
>>>> Almost always, when this happens, it's because the name of the
>>>> reference sequence in the BAM file is different from the names of the
>>>> reference sequences in the seq/refSeqs.json file.  If that's the case and
>>>> you have the very fresh 1.16.10 release, you can use the
>>>> customRefRename and replaceRefRename  options described here:
>>>> https://jbrowse.org/docs/global_options.html.  If you need to go down
>>>> that path, and enlightenment doesn't immediately strike you, please feel
>>>> free to write back to this list.
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Thu, Sep 24, 2020 at 2:56 PM JM C <jua...@gm...> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I'm setting up a demo jbrowse with a bam file with .csi index.
>>>>>
>>>>>
>>>>> http://165.227.95.85/jbrowse/?loc=2A%3A651960001..674020000&tracks=b19&highlight=
>>>>>
>>>>> I can see the track and got no errors but the track is empty in the
>>>>> browser. Not sure how to troubleshoot this, any suggestions?
>>>>>
>>>>>
>>>>> --
>>>>> *Juan Manuel Crescente*
>>>>>
>>>>> This message is confidential. You may not copy this message or
>>>>> disclose its contents to anyone.
>>>>> Please consider the environment before printing this email.
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>> dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>

Re: [Gmod-ajax] Problem with BAM .csi index file

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

Note also, JBrowse could be programmed to support this out of the box
without a custom configuration, we are just trying to help find a solution
that works for you, with what we have now :)

To see jbrowse's current capabilities for this see
https://github.com/GMOD/jbrowse/blob/master/tests/js_tests/spec/RegularizeRefSeqs.spec.js

The chr2A/2A does not work but we could add that to our test matrix, etc

-Colin

On Thu, Sep 24, 2020 at 7:25 PM Colin <col...@gm...> wrote:

> While it's nice igv loads it, but they are likely doing similar "smoothing
> over" the differences in refname between your bam and the reference genome.
>
> Most programs do not do any of this smoothing over of this and so it is
> generally better to ensure your data is using the same reference sequence
> names
>
> Try:
>
> samtools view
> http://165.227.95.85/jbrowse/data/Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam
> 2A
>
> This fails because your BAM file uses chr2A not 2A.
>
> As noted above, jbrowse can also try to help this case too, but requires
> the replaceRefRename callback
>
> -Colin
>
> On Thu, Sep 24, 2020 at 7:03 PM JM C <jua...@gm...> wrote:
>
>> HI Scott
>>
>> thank you for your reply. I see your point in there. This shouldn't be
>> the case since I'm using the same genome with the same bam file in igv and
>> it's working correctly.
>>
>> This is my track config btw
>>
>> [ tracks.bam_biointa_2002 ]
>> storeClass=JBrowse/Store/SeqFeature/BAM
>>
>> urlTemplate=Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam
>> category=BAM
>> type=Alignments2
>> key=Biointa 2002
>>
>> csiUrlTemplate=Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam.csi
>>
>>
>>
>>
>> --
>> *Juan Manuel Crescente*
>>
>> This message is confidential. You may not copy this message or disclose
>> its contents to anyone.
>> Please consider the environment before printing this email.
>>
>>
>> On Thu, Sep 24, 2020 at 7:10 PM Scott Cain <sc...@sc...> wrote:
>>
>>> Hi Juan,
>>>
>>> Almost always, when this happens, it's because the name of the reference
>>> sequence in the BAM file is different from the names of the reference
>>> sequences in the seq/refSeqs.json file.  If that's the case and you have
>>> the very fresh 1.16.10 release, you can use the customRefRename and
>>> replaceRefRename  options described here:
>>> https://jbrowse.org/docs/global_options.html.  If you need to go down
>>> that path, and enlightenment doesn't immediately strike you, please feel
>>> free to write back to this list.
>>>
>>> Scott
>>>
>>>
>>> On Thu, Sep 24, 2020 at 2:56 PM JM C <jua...@gm...> wrote:
>>>
>>>> Hi,
>>>>
>>>> I'm setting up a demo jbrowse with a bam file with .csi index.
>>>>
>>>>
>>>> http://165.227.95.85/jbrowse/?loc=2A%3A651960001..674020000&tracks=b19&highlight=
>>>>
>>>> I can see the track and got no errors but the track is empty in the
>>>> browser. Not sure how to troubleshoot this, any suggestions?
>>>>
>>>>
>>>> --
>>>> *Juan Manuel Crescente*
>>>>
>>>> This message is confidential. You may not copy this message or disclose
>>>> its contents to anyone.
>>>> Please consider the environment before printing this email.
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] Problem with BAM .csi index file

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

While it's nice igv loads it, but they are likely doing similar "smoothing
over" the differences in refname between your bam and the reference genome.

Most programs do not do any of this smoothing over of this and so it is
generally better to ensure your data is using the same reference sequence
names

Try:

samtools view
http://165.227.95.85/jbrowse/data/Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam
2A

This fails because your BAM file uses chr2A not 2A.

As noted above, jbrowse can also try to help this case too, but requires
the replaceRefRename callback

-Colin

On Thu, Sep 24, 2020 at 7:03 PM JM C <jua...@gm...> wrote:

> HI Scott
>
> thank you for your reply. I see your point in there. This shouldn't be the
> case since I'm using the same genome with the same bam file in igv and it's
> working correctly.
>
> This is my track config btw
>
> [ tracks.bam_biointa_2002 ]
> storeClass=JBrowse/Store/SeqFeature/BAM
>
> urlTemplate=Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam
> category=BAM
> type=Alignments2
> key=Biointa 2002
>
> csiUrlTemplate=Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam.csi
>
>
>
>
> --
> *Juan Manuel Crescente*
>
> This message is confidential. You may not copy this message or disclose
> its contents to anyone.
> Please consider the environment before printing this email.
>
>
> On Thu, Sep 24, 2020 at 7:10 PM Scott Cain <sc...@sc...> wrote:
>
>> Hi Juan,
>>
>> Almost always, when this happens, it's because the name of the reference
>> sequence in the BAM file is different from the names of the reference
>> sequences in the seq/refSeqs.json file.  If that's the case and you have
>> the very fresh 1.16.10 release, you can use the customRefRename and
>> replaceRefRename  options described here:
>> https://jbrowse.org/docs/global_options.html.  If you need to go down
>> that path, and enlightenment doesn't immediately strike you, please feel
>> free to write back to this list.
>>
>> Scott
>>
>>
>> On Thu, Sep 24, 2020 at 2:56 PM JM C <jua...@gm...> wrote:
>>
>>> Hi,
>>>
>>> I'm setting up a demo jbrowse with a bam file with .csi index.
>>>
>>>
>>> http://165.227.95.85/jbrowse/?loc=2A%3A651960001..674020000&tracks=b19&highlight=
>>>
>>> I can see the track and got no errors but the track is empty in the
>>> browser. Not sure how to troubleshoot this, any suggestions?
>>>
>>>
>>> --
>>> *Juan Manuel Crescente*
>>>
>>> This message is confidential. You may not copy this message or disclose
>>> its contents to anyone.
>>> Please consider the environment before printing this email.
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Problem with BAM .csi index file

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

Yes, exactly.  I downloaded the bam file and found that the reference
sequences are named like 'chr1A', so Colin's suggestion should do the trick.

On Thu, Sep 24, 2020 at 3:52 PM Colin <col...@gm...> wrote:

> As Scott said, timely question. Standardizing the data files ref names is
> normally good but jbrowse does try to smooth over things like chr1 vs 1 but
> doesn't have chr1A vs 1A right now
>
> In JBrowse 1.16.10, you could try putting this in the jbrowse.conf below
> the [GENERAL] tag
>
>
> replaceRefRename = function(ref) { return
> ref.toLowerCase().replace('chr','') }
>
>
> -Colin
>
> On Thu, Sep 24, 2020 at 6:16 PM Scott Cain <sc...@sc...> wrote:
>
>> Hi Juan,
>>
>> Almost always, when this happens, it's because the name of the reference
>> sequence in the BAM file is different from the names of the reference
>> sequences in the seq/refSeqs.json file.  If that's the case and you have
>> the very fresh 1.16.10 release, you can use the customRefRename and
>> replaceRefRename  options described here:
>> https://jbrowse.org/docs/global_options.html.  If you need to go down
>> that path, and enlightenment doesn't immediately strike you, please feel
>> free to write back to this list.
>>
>> Scott
>>
>>
>> On Thu, Sep 24, 2020 at 2:56 PM JM C <jua...@gm...> wrote:
>>
>>> Hi,
>>>
>>> I'm setting up a demo jbrowse with a bam file with .csi index.
>>>
>>>
>>> http://165.227.95.85/jbrowse/?loc=2A%3A651960001..674020000&tracks=b19&highlight=
>>>
>>> I can see the track and got no errors but the track is empty in the
>>> browser. Not sure how to troubleshoot this, any suggestions?
>>>
>>>
>>> --
>>> *Juan Manuel Crescente*
>>>
>>> This message is confidential. You may not copy this message or disclose
>>> its contents to anyone.
>>> Please consider the environment before printing this email.
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] Problem with BAM .csi index file

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

As Scott said, timely question. Standardizing the data files ref names is
normally good but jbrowse does try to smooth over things like chr1 vs 1 but
doesn't have chr1A vs 1A right now

In JBrowse 1.16.10, you could try putting this in the jbrowse.conf below
the [GENERAL] tag


replaceRefRename = function(ref) { return
ref.toLowerCase().replace('chr','') }


-Colin

On Thu, Sep 24, 2020 at 6:16 PM Scott Cain <sc...@sc...> wrote:

> Hi Juan,
>
> Almost always, when this happens, it's because the name of the reference
> sequence in the BAM file is different from the names of the reference
> sequences in the seq/refSeqs.json file.  If that's the case and you have
> the very fresh 1.16.10 release, you can use the customRefRename and
> replaceRefRename  options described here:
> https://jbrowse.org/docs/global_options.html.  If you need to go down
> that path, and enlightenment doesn't immediately strike you, please feel
> free to write back to this list.
>
> Scott
>
>
> On Thu, Sep 24, 2020 at 2:56 PM JM C <jua...@gm...> wrote:
>
>> Hi,
>>
>> I'm setting up a demo jbrowse with a bam file with .csi index.
>>
>>
>> http://165.227.95.85/jbrowse/?loc=2A%3A651960001..674020000&tracks=b19&highlight=
>>
>> I can see the track and got no errors but the track is empty in the
>> browser. Not sure how to troubleshoot this, any suggestions?
>>
>>
>> --
>> *Juan Manuel Crescente*
>>
>> This message is confidential. You may not copy this message or disclose
>> its contents to anyone.
>> Please consider the environment before printing this email.
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Problem with BAM .csi index file

[JM C <jua...@gm...>]

HI Scott

thank you for your reply. I see your point in there. This shouldn't be the
case since I'm using the same genome with the same bam file in igv and it's
working correctly.

This is my track config btw

[ tracks.bam_biointa_2002 ]
storeClass=JBrowse/Store/SeqFeature/BAM
urlTemplate=Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam
category=BAM
type=Alignments2
key=Biointa 2002
csiUrlTemplate=Biointa2002_S116_L003_R1_001_bwa_iwgscv1ABUK_20200719.sorted.rmdup.bam.csi




--
*Juan Manuel Crescente*

This message is confidential. You may not copy this message or disclose its
contents to anyone.
Please consider the environment before printing this email.


On Thu, Sep 24, 2020 at 7:10 PM Scott Cain <sc...@sc...> wrote:

> Hi Juan,
>
> Almost always, when this happens, it's because the name of the reference
> sequence in the BAM file is different from the names of the reference
> sequences in the seq/refSeqs.json file.  If that's the case and you have
> the very fresh 1.16.10 release, you can use the customRefRename and
> replaceRefRename  options described here:
> https://jbrowse.org/docs/global_options.html.  If you need to go down
> that path, and enlightenment doesn't immediately strike you, please feel
> free to write back to this list.
>
> Scott
>
>
> On Thu, Sep 24, 2020 at 2:56 PM JM C <jua...@gm...> wrote:
>
>> Hi,
>>
>> I'm setting up a demo jbrowse with a bam file with .csi index.
>>
>>
>> http://165.227.95.85/jbrowse/?loc=2A%3A651960001..674020000&tracks=b19&highlight=
>>
>> I can see the track and got no errors but the track is empty in the
>> browser. Not sure how to troubleshoot this, any suggestions?
>>
>>
>> --
>> *Juan Manuel Crescente*
>>
>> This message is confidential. You may not copy this message or disclose
>> its contents to anyone.
>> Please consider the environment before printing this email.
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

Re: [Gmod-ajax] Problem with BAM .csi index file

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

Hi Juan,

Almost always, when this happens, it's because the name of the reference
sequence in the BAM file is different from the names of the reference
sequences in the seq/refSeqs.json file.  If that's the case and you have
the very fresh 1.16.10 release, you can use the customRefRename and
replaceRefRename  options described here:
https://jbrowse.org/docs/global_options.html.  If you need to go down that
path, and enlightenment doesn't immediately strike you, please feel free to
write back to this list.

Scott


On Thu, Sep 24, 2020 at 2:56 PM JM C <jua...@gm...> wrote:

> Hi,
>
> I'm setting up a demo jbrowse with a bam file with .csi index.
>
>
> http://165.227.95.85/jbrowse/?loc=2A%3A651960001..674020000&tracks=b19&highlight=
>
> I can see the track and got no errors but the track is empty in the
> browser. Not sure how to troubleshoot this, any suggestions?
>
>
> --
> *Juan Manuel Crescente*
>
> This message is confidential. You may not copy this message or disclose
> its contents to anyone.
> Please consider the environment before printing this email.
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] Problem with BAM .csi index file

[JM C <jua...@gm...>]

Hi,

I'm setting up a demo jbrowse with a bam file with .csi index.

http://165.227.95.85/jbrowse/?loc=2A%3A651960001..674020000&tracks=b19&highlight=

I can see the track and got no errors but the track is empty in the
browser. Not sure how to troubleshoot this, any suggestions?


--
*Juan Manuel Crescente*

This message is confidential. You may not copy this message or disclose its
contents to anyone.
Please consider the environment before printing this email.

[Gmod-ajax] JBrowse 1.16.10 maintenance release

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

Hi all,
I'm pleased to announce a new update for JBrowse. This release contains
changes that fixes a bug rendering SNPs from reads with multiple CIGAR
skips, e.g. Iso-Seq. It also includes a modest speedup for long reads,
automatic generation of MD tags for BAM, and more. Please see the changelog
below!


   - JBrowse-1.16.10.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.10-release/JBrowse-1.16.10.zip>
-
   minified release
   - JBrowse-1.16.10-dev.zip
   <https://github.com/GMOD/jbrowse/archive/1.16.10-release.zip> - use this
   if you modify jbrowse source code or use plugins
   - JBrowse-1.16.10-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.10-release/JBrowse-1.16.10-desktop-win32-x64.zip>
   - JBrowse-1.16.10-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.10-release/JBrowse-1.16.10-desktop-linux-x64.zip>
   - JBrowse-1.16.10-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.10-release/JBrowse-1.16.10-desktop-darwin-x64.zip>


Blog post https://jbrowse.org/blog/2020/09/24/jbrowse-1-16-10.html

Let us know if you have any questions, and stay safe out there :)
Minor improvements

   -

   Added an optimization for BAM that helps for long reads especially (
   @cmdcolin <https://github.com/cmdcolin>)
   -

   Added generation of the MD tag if none is specified in BAM (issue #1022,
   @cmdcolin <https://github.com/cmdcolin>)
   -

   Added customRefRename and replaceRefRename global configs for extending
   and replacing ref renaming functionality respectively. Ref renaming helps
   things like chrM and chrMT to be loaded onto the same chromosome in jbrowse
   (@cmdcolin <https://github.com/cmdcolin>, issue #1506
   <https://github.com/gmod/jbrowse/pull/1506>)
   -

   Added support for a -f option for setup.sh. This option causes setup to
   skip installing perl prerequisites and setting up sample data. It is
   primarily intended to support faster builds in a Docker context. (
   @scottcain <https://github.com/scottcain>)

<https://jbrowse.org/blog/2020/09/24/jbrowse-1-16-10.html#bug-fixes>Bug
fixes

   -

   Fix the display of mismatches from hard clipped BAM sequences (issue
   #1513 <https://github.com/gmod/jbrowse/pull/1513>)
   -

   Fix ability to use tracks from Open track dialog in combination tracks.
   Thanks to Sonny Arora for the repo (issue #1536
   <https://github.com/gmod/jbrowse/pull/1536>)
   -

   Fix mismatch/SNP calculation for reads with multiple skips, e.g. Iso-Seq
   (@cmdcolin <https://github.com/cmdcolin>)

Re: [Gmod-ajax] unable to install Jbrowse

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

Hi Sofia,

Generally because of the way JBrowse works, you need to use a web server to
serve the JBrowse files.  Directly accessing the index file in your file
system won't work.  See
https://jbrowse.org/docs/faq.html#what-webserver-is-needed-for-jbrowse for
more information, and feel free to ask for additional help on this list.

Scott


On Fri, Sep 18, 2020 at 9:02 AM Rigou Sofia <sof...@ig...>
wrote:

> Hi,
>
> I am having troubles installing Jbrowse 1.16.9. This is the message I get
> when I try to load the yeast example :
> "Congratulations, JBrowse is on the web!
>
> However, JBrowse could not start, either because it has not yet been
> configured and loaded with data, or because of an error.
>
> If this is your first time running JBrowse, click here to follow the
> Quick-start Tutorial to show your data in JBrowse.
>
> Otherwise, please refer to the following resources for help in setting up
> JBrowse to show your data.
>
>    - Quick-start tutorial - get your data visible quickly with minimum
>    fuss
>    - JBrowse Configuration Guide
>    <http://gmod.org/wiki/JBrowse_Configuration_Guide> - a comprehensive
>    reference
>    - JBrowse wiki main page <http://gmod.org/wiki/JBrowse>
>    - biodb-to-json.pl configuration reference
>    - HTMLFeatures CSS class reference - prepackaged styles (CSS classes)
>    for HTMLFeatures tracks
>
> Error message(s):
> RequestError: Unable to load
> file:///var/www/html/JBrowse-1.16.9/jbrowse.conf?v=0.8032247523260153
> status: 0.
> "
> I read on github that the solution to this problem was not found yet... Do
> you happen to know what it could be due to and how to solve it ?
> Thank you very much in advance,
>
> --
> -----------------------------------------------------
> Sofia Rigou
> Doctorante
> CNRS - AMU - IGS -UMR 7256
> Information Génomique & Structurale
> Tél. 04.91.82.54.23
> -----------------------------------------------------
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] unable to install Jbrowse

[Rigou S. <sof...@ig...>]

Hi,

I am having troubles installing Jbrowse 1.16.9. This is the message I 
get when I try to load the yeast example :


  "Congratulations, JBrowse is on the web!

However, JBrowse could not start, either because it has not yet been 
configured and loaded with data, or because of an error.

If this is your first time running JBrowse, click here to follow the 
Quick-start Tutorial to show your data in JBrowse.

Otherwise, please refer to the following resources for help in setting 
up JBrowse to show your data.

  * Quick-start tutorial - get your data visible quickly with minimum fuss
  * JBrowse Configuration Guide
    <http://gmod.org/wiki/JBrowse_Configuration_Guide> - a comprehensive
    reference
  * JBrowse wiki main page <http://gmod.org/wiki/JBrowse>
  * |biodb-to-json.pl| configuration reference
  * HTMLFeatures CSS class reference - prepackaged styles (CSS classes)
    for HTMLFeatures tracks


    Error message(s):

RequestError: Unable to load 
file:///var/www/html/JBrowse-1.16.9/jbrowse.conf?v=0.8032247523260153 
status: 0.
"
I read on github that the solution to this problem was not found yet... 
Do you happen to know what it could be due to and how to solve it ?
Thank you very much in advance,

-- 
-----------------------------------------------------
Sofia Rigou
Doctorante
CNRS - AMU - IGS -UMR 7256
Information Génomique & Structurale
Tél. 04.91.82.54.23
-----------------------------------------------------

Re: [Gmod-ajax] Add bam with corresponding csi index file

[SAPET, F. <fre...@li...>]

Hi

You can use the "csiUrlTemplate" in the config.

Fred

De : Cyril Libourel <cyr...@lr...>
Envoyé : lundi 14 septembre 2020 14:20
À : gmo...@li...
Objet : [Gmod-ajax] Add bam with corresponding csi index file

Helo,

I am working on Barley genome. This species have long chromosomes leading to use csi index files for BAM.
I tried to put BAM + .csi file in my jbrowse but I get error telling me that there is no index file.
What can I do to "force" jbrowse to use the csi file as index?

Thank you very much in advance

Cyril

Cyril Libourel, Ph.D.
Postdoctoral researcher
Pôle de Biotechnologies Végétales
Laboratoire de Recherche en Sciences Végétales
UMR 5546 CNRS-UPS
24 Chemin de Borde Rouge
31326 Castanet Tolosan
FRANCE

https://www.lrsv.ups-tlse.fr/equipes-de-recherche/symbiose-mycorhizienne-et-signalisation-cellulaire/

Re: [Gmod-ajax] No exons and introns present in gene model​

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

One thing to try is to use --trackType CanvasFeatures

The default, with no trackType specified, is HTMLFeatures

Here is a short summary of HTMLFeatures vs CanvasFeatures

http://gmod.org/wiki/JBrowse_FAQ#What_is_the_difference_between_CanvasFeatures_and_HTMLFeatures.3F

If you are interested in configuring HTMLFeatures properly you might add
--type mRNA instead of --type gene, because HTMLFeatures works properly
when loaded at the transcript level, CanvasFeatures can be loaded at the
gene level though


-Colin

On Wed, Sep 16, 2020 at 10:43 AM 李会 <lih...@ma...> wrote:

> Dear JBrowse staff,
>
>
> We are using Jbrowse to configure the structural characteristics of our
> genome, but we found that the exons and introns are not present in the
> gene model. GFF format, configuration file and commands used in our
> program are summarized in the attachment, including problems we can not solve.
> Please check the attached file and help us to get the correct gene model
> (configuration) with exons and introns.
>
>
>
> Sincerely,
>
> Hui Li
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Add bam with corresponding csi index file

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

Can you describe how you are putting the BAM in JBrowse?

Is it through the Open track dialog box or manually editing the config?

I tested adding via the Open track dialog and it seemed to work

Manually editing it in the config requires adding the config
parameter "csiUrlTemplate": "yourfile.bam.csi" with "urlTemplate":
"yourfile.bam"

Also which version of jbrowse is being used?

Thanks,
-Colin

On Wed, Sep 16, 2020 at 10:43 AM Cyril Libourel <
cyr...@lr...> wrote:

> Helo,
>
>
>
> I am working on Barley genome. This species have long chromosomes leading
> to use csi index files for BAM.
>
> I tried to put BAM + .csi file in my jbrowse but I get error telling me
> that there is no index file.
>
> What can I do to “force” jbrowse to use the csi file as index?
>
>
>
> Thank you very much in advance
>
>
>
> Cyril
>
>
>
> Cyril Libourel, Ph.D.
>
> Postdoctoral researcher
>
> Pôle de Biotechnologies Végétales
>
> Laboratoire de Recherche en Sciences Végétales
>
> UMR 5546 CNRS-UPS
>
> 24 Chemin de Borde Rouge
>
> 31326 Castanet Tolosan
>
> FRANCE
>
>
>
>
> https://www.lrsv.ups-tlse.fr/equipes-de-recherche/symbiose-mycorhizienne-et-signalisation-cellulaire/
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] No exons and introns present in gene model​

[李会 <lih...@ma...>]

Dear JBrowse staff,





We are using Jbrowse to configure the structural characteristics of our genome, but we found that the exons and introns are not present in the gene model. GFF format, configuration file and commands used in our program are summarized in the attachment,including problems we can not solve. Please check the attached file and help us to get the correctgene model (configuration) with exons and introns.







Sincerely,

Hui Li

[Gmod-ajax] Increasing descritpion cut off

[Michał T. L. <m.t...@gm...>]

Hi all,
How is it possible to make the description visible in full length?

ID=gene.100.0.2.p1;Note=SeqStart:M AAseqLen:441 CDSseqLen:441
CDS:7%2CExon:7 3UTR:1 5UTR:1 cov:1.486100
RPKM:0.030600;Parent=gene.100.0

Thank you in advance,

Michal

[Gmod-ajax] Add bam with corresponding csi index file

[Cyril L. <cyr...@lr...>]

Helo,

 

I am working on Barley genome. This species have long chromosomes leading to
use csi index files for BAM.

I tried to put BAM + .csi file in my jbrowse but I get error telling me that
there is no index file.

What can I do to “force” jbrowse to use the csi file as index?

 

Thank you very much in advance

 

Cyril

 

Cyril Libourel, Ph.D.

Postdoctoral researcher

Pôle de Biotechnologies Végétales

Laboratoire de Recherche en Sciences Végétales

UMR 5546 CNRS-UPS

24 Chemin de Borde Rouge

31326 Castanet Tolosan

FRANCE

 

 
<https://www.lrsv.ups-tlse.fr/equipes-de-recherche/symbiose-mycorhizienne-et
-signalisation-cellulaire/>
https://www.lrsv.ups-tlse.fr/equipes-de-recherche/symbiose-mycorhizienne-et-
signalisation-cellulaire/

 

Re: [Gmod-ajax] JBrowse substring name search

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

Hi there,
One option: make sprtn a separate field in the GFF. So maybe reformat the
GFF column 9 like this

ID=XB22065605;provisional=sprtn

Then use bin/generate-names.pl --nameAttributes id,provisional

Other option https://github.com/elsiklab/jbrowse_elasticsearch which does
true full text indexing but requires server side setup of elasticsearch

-Colin

On Mon, Aug 31, 2020 at 2:04 PM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
>
>
> I was curious if in JBrowse when generating the name indexes for the
> genes, is there a way to make it possible to retrieve genes in the browser
> search by searching for a substring within the gene symbol, as opposed to
> always a prefix that starts from the beginning of the gene symbol?  The
> reason I ask is, for some of our Xenopus genes which are not annotated
> fully yet, we have a provisional gene format which consists of 2 pieces
> like this one for example:
>
>
>
> XB22065605 [provisional:sprtn]
>
>
>
> I could be mistaken, but it appears that in JBrowse you can search for
> many pieces of the gene symbol string, as long as you start from the 1st
> character, so in this example, begin typing ‘XB….’ to find it.  In this
> example it would be valuable for us to search for the provisional symbol in
> this string so ‘sprtn’ and find the result, but it doesn’t work.  Is there
> any method we can use to generate those types of name indexes?  I know
> there’s a –completionLimit parameter which retrieve more completions of the
> prefix for the gene symbol but I assume all those auto-completions still
> require the search term to begin with the first few characters of the
> string.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building – University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse substring name search

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

Hello,

I was curious if in JBrowse when generating the name indexes for the genes, is there a way to make it possible to retrieve genes in the browser search by searching for a substring within the gene symbol, as opposed to always a prefix that starts from the beginning of the gene symbol?  The reason I ask is, for some of our Xenopus genes which are not annotated fully yet, we have a provisional gene format which consists of 2 pieces like this one for example:

XB22065605 [provisional:sprtn]

I could be mistaken, but it appears that in JBrowse you can search for many pieces of the gene symbol string, as long as you start from the 1st character, so in this example, begin typing 'XB....' to find it.  In this example it would be valuable for us to search for the provisional symbol in this string so 'sprtn' and find the result, but it doesn't work.  Is there any method we can use to generate those types of name indexes?  I know there's a -completionLimit parameter which retrieve more completions of the prefix for the gene symbol but I assume all those auto-completions still require the search term to begin with the first few characters of the string.

Thanks,

Vaneet

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