jbrowse: change feature density to gene structure

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

jbrowse: change feature density to gene structure

Pengcheng Yang

Hi miners,

Following [1], the gene will be displayed, but in the feature density model. According to the JBrowse documentation, the feature density display will disappear when there are few genes in the shown region. However, the track for gene was unchanged when there was only one gene in the region [2]. But the Exon and Repeat region tracks displayed detailed regions when the window was zoomed in [3]. What could this be caused by?

Best,

Pengcheng


[1] http://locustmine.org/jbrowse/JBrowse-1.14.0/?data=http://locustmine.org:8080//testmine/service/jbrowse/config/7004&loc=scaffold2825:2166013..2369874&tracks=LocustMine-7004-Gene

[2] zoom out view


[3] zoom in view


_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: jbrowse: change feature density to gene structure

Justin Clark-Casey-2
Unfortunately, I'm not sure we can give a definitive answer - I don't
know if any of the mines we've hosted here at Cambridge now or in the
past have really been using the JBrowse integration.  Perhaps someone
else on the list can help.

Or you might be able to ask JBrowse directly, though the default
InterMine integration has it pull data from a set of InterMine web
services and I'm not sure how extensively that's supported in comparison
to using data read in directly by JBrowse from the filesystem.

-- Justin

On 2018-05-03 17:31, Pengcheng Yang wrote:

> Hi miners,
>
> Following [1], the gene will be displayed, but in the feature density
> model. According to the JBrowse documentation, the feature density
> display will disappear when there are few genes in the shown region.
> However, the track for gene was unchanged when there was only one gene
> in the region [2]. But the Exon and Repeat region tracks displayed
> detailed regions when the window was zoomed in [3]. What could this be
> caused by?
>
> Best,
>
> Pengcheng
>
> [1]
> http://locustmine.org/jbrowse/JBrowse-1.14.0/?data=http://locustmine.org:8080//testmine/service/jbrowse/config/7004&loc=scaffold2825:2166013..2369874&tracks=LocustMine-7004-Gene
>
>
> [2] zoom out view
>
> [3] zoom in view
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: jbrowse: change feature density to gene structure

Gos Micklem-3

I would definitely contact the JBrowse developers - we would like to know what you learn
so perhaps keep us copied in.

Best wishes,

Gos


On May 04 2018, [hidden email] wrote:

> Unfortunately, I'm not sure we can give a definitive answer - I don't know
> if any of the mines we've hosted here at Cambridge now or in the past have
> really been using the JBrowse integration.  Perhaps someone else on the list
> can help.
>
> Or you might be able to ask JBrowse directly, though the default InterMine
> integration has it pull data from a set of InterMine web services and I'm
> not sure how extensively that's supported in comparison to using data read
> in directly by JBrowse from the filesystem.
>
> -- Justin
>
> On 2018-05-03 17:31, Pengcheng Yang wrote:
> > Hi miners,
> >
> > Following [1], the gene will be displayed, but in the feature density
> > model. According to the JBrowse documentation, the feature density
> > display will disappear when there are few genes in the shown region.
> > However, the track for gene was unchanged when there was only one gene
> > in the region [2]. But the Exon and Repeat region tracks displayed
> > detailed regions when the window was zoomed in [3]. What could this be
> > caused by?
> >
> > Best,
> >
> > Pengcheng
> >
> > [1]
> > http://locustmine.org/jbrowse/JBrowse-1.14.0/?data=http://locustmine.org:8080//testmine/service/jbrowse/config/7004&loc=scaffold2825:2166013..2369874&tracks=LocustMine-7004-Gene
> >
> >
> > [2] zoom out view
> >
> > [3] zoom in view
> > _______________________________________________
> > dev mailing list
> > [hidden email]
> > https://lists.intermine.org/mailman/listinfo/dev
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: jbrowse: change feature density to gene structure

Sam Hokin-3
I use the plain vanilla JBrowse functionality, where I do _not_ configure JBrowse or store any data directly accessible by JBrowse
on its server; JBrowse pulls it all from the mine via the IM API as Justin mentioned. Dunno if that helps, but I'm not sure very
many miners use the minimalist JBrowse implementation like me. So the beany mines are an example of that.

A good alternative to look at is the ThaleMine/MedicMine implementation, where JBrowse is run the traditional way with at least some
data accessed locally. Plus, Vivek wrote a number of improvements to both the front end and JSP. See:

https://github.com/Arabidopsis-Information-Portal/jbrowse
https://github.com/Arabidopsis-Information-Portal/thalemine/blob/master/webapp/src/main/webapp/model/jbrowseDisplayer.jsp

https://github.com/jcvi-plant-genomics/jbrowse
https://github.com/jcvi-plant-genomics/medicmine/blob/master/webapp/src/main/webapp/model/jbrowseDisplayer.jsp

(Vivek has left JCVI in Maryland and is now at Illumina in San Diego, but I hope he will continue to monitor this list when his new
job/life settles down. Because we need him. :)

> On May 04 2018, [hidden email] wrote:
>> Unfortunately, I'm not sure we can give a definitive answer - I don't know
>> if any of the mines we've hosted here at Cambridge now or in the past have
>> really been using the JBrowse integration.  Perhaps someone else on the list
>> can help.
>>
>> Or you might be able to ask JBrowse directly, though the default InterMine
>> integration has it pull data from a set of InterMine web services and I'm
>> not sure how extensively that's supported in comparison to using data read
>> in directly by JBrowse from the filesystem.
>>
>> -- Justin
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev