[Gmod-ajax] color by CDS frame?

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[Gmod-ajax] color by CDS frame?

Loraine Guéguen
Hi,

Can we color genes by CDS frame in a feature track?
like in Apollo for the annotation track (menu "View" > "Color by CDS frame")

Thanks,

Loraine



--
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/


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Re: color by CDS frame?

nathandunn

Loraine,

You should be able to use the public track option for organisms with Apollo to simulate JBrowse which has the color on by default in the master branch (this can be configured off as well).  Though I realize this alters the track types, it *should* work with most plugins.  

If you do need to do this in JBrowse, keep in mind we had to fix ours recently (also on master) as there were errors in the way Apollo (and also JBrowse) draw the minus strand for the coding proteins if you want to employ similar coloring.     Apollo uses its own SequenceTrack object so you can’t pick up those fixes:


I think this would be a great standalone plugin, but you would definitely want to fix the minus strand bug, first. 

Nathan

On Jul 31, 2017, at 1:32 AM, Loraine Guéguen <[hidden email]> wrote:

Hi,

Can we color genes by CDS frame in a feature track?
like in Apollo for the annotation track (menu "View" > "Color by CDS frame")

Thanks,

Loraine



--
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/


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Re: color by CDS frame?

Loraine Guéguen
Hi Nathan,

I am not sure to understand ("public track option" ?)

It is for JBrowse, without Apollo.
I have an evidence track containing CDS features (and ARN), with this configuration in trackList.json :
"trackType" : "CanvasFeatures"
"storeClass" : "JBrowse/Store/SeqFeature/NCList"

This is not essential but I was wondering if it is possible to color the CDS by their frame (with configuration into trackList.json...)


Loraine



Le 02/08/2017 06:46, Nathan Dunn a écrit :

Loraine,

You should be able to use the public track option for organisms with Apollo to simulate JBrowse which has the color on by default in the master branch (this can be configured off as well).  Though I realize this alters the track types, it *should* work with most plugins.  

If you do need to do this in JBrowse, keep in mind we had to fix ours recently (also on master) as there were errors in the way Apollo (and also JBrowse) draw the minus strand for the coding proteins if you want to employ similar coloring.     Apollo uses its own SequenceTrack object so you can’t pick up those fixes:


I think this would be a great standalone plugin, but you would definitely want to fix the minus strand bug, first. 

Nathan

On Jul 31, 2017, at 1:32 AM, Loraine Guéguen <[hidden email]> wrote:

Hi,

Can we color genes by CDS frame in a feature track?
like in Apollo for the annotation track (menu "View" > "Color by CDS frame")

Thanks,

Loraine



--
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/


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-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/


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Re: color by CDS frame?

Colin
I thought this would be a good feature to have also. I thought it might help to wrap it up in a plugin, so I made this :) https://github.com/cmdcolin/colorbycds

Currently if you enable it, then it is "always on", it might be possible to make it optional though. It also is configured for canvasfeatures, but htmlfeatures might be possible also.

-Colin

On Wed, Aug 2, 2017 at 9:35 AM, Loraine Guéguen <[hidden email]> wrote:
Hi Nathan,

I am not sure to understand ("public track option" ?)

It is for JBrowse, without Apollo.
I have an evidence track containing CDS features (and ARN), with this configuration in trackList.json :
"trackType" : "CanvasFeatures"
"storeClass" : "JBrowse/Store/SeqFeature/NCList"

This is not essential but I was wondering if it is possible to color the CDS by their frame (with configuration into trackList.json...)


Loraine




Le 02/08/2017 06:46, Nathan Dunn a écrit :

Loraine,

You should be able to use the public track option for organisms with Apollo to simulate JBrowse which has the color on by default in the master branch (this can be configured off as well).  Though I realize this alters the track types, it *should* work with most plugins.  

If you do need to do this in JBrowse, keep in mind we had to fix ours recently (also on master) as there were errors in the way Apollo (and also JBrowse) draw the minus strand for the coding proteins if you want to employ similar coloring.     Apollo uses its own SequenceTrack object so you can’t pick up those fixes:


I think this would be a great standalone plugin, but you would definitely want to fix the minus strand bug, first. 

Nathan

On Jul 31, 2017, at 1:32 AM, Loraine Guéguen <[hidden email]> wrote:

Hi,

Can we color genes by CDS frame in a feature track?
like in Apollo for the annotation track (menu "View" > "Color by CDS frame")

Thanks,

Loraine



--
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: <a href="tel:+33%202%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/


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-- 
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: <a href="tel:+33%202%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/


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