ORF viewer track

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ORF viewer track

Alan Tracey
Hi


I'm working to annotate the Schistosoma mansoni genome.  I think Apollo
could benefit from having a collapsible track to allow the viewing of
ORFs.  Currently, I use Artemis in conjunction with Apollo to provide
this missing information, but would love to be able to just use Apollo. 
I really like using Apollo - it has some very nice functionality.


Thanks,

Alan



--
 The Wellcome Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.




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Re: ORF viewer track

nathandunn

We have collapsible tracks (see below).  Not sure if this is what you meant, though.   

If you have a specific screenshot for the view you want, that would be helpful. 

Thanks, 

Nathan







On Jan 19, 2018, at 6:46 AM, Alan Tracey <[hidden email]> wrote:

Hi


I'm working to annotate the Schistosoma mansoni genome.  I think Apollo could benefit from having a collapsible track to allow the viewing of ORFs.  Currently, I use Artemis in conjunction with Apollo to provide this missing information, but would love to be able to just use Apollo.  I really like using Apollo - it has some very nice functionality.


Thanks,

Alan



--
The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.



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Re: ORF viewer track

nathandunn

Allan, this is very helpful.  I opened this issue up:


We provide something like this in Apollo (which I’m going to fix with https://github.com/GMOD/Apollo/pull/1852) and JBrowse, however, they typically hide when zoomed out.   I see two options:

1 - create a track that always / only shows the potential ORFs (and only the ORFs, no sequence)
2 - make the sequence track display the ORFs only when zoomed out

You can put any thoughts here or on the issue (1853) directly.  

Cheers,

Nathan


On Jan 19, 2018, at 12:24 PM, Alan Tracey <[hidden email]> wrote:

Hi Nathan

Just forwarding on a mail that I sent to colleagues earlier today - hopefully this explains what I'm looking for.


Many thanks,

Alan




Hi Michael


I think what I'm looking for is a view like what I paste below, which can be collapsed/expanded when required and whose coordinates mirror those of the current view, so different levels of zoom would change the view.  Just to give information of the potential ORFs rather than those already incorporated into the gene model.  Does that make sense?

<ceenikloglaahehh.png>


On 19/01/18 15:57, Faye Rodgers wrote:
Ah- do you mean the colour by cds which we already have? Or something else?

 

From: Michael Paulini [hidden email]
Date: Friday, January 19, 2018 at 15:45
To: Faye Rodgers [hidden email]
Cc: Alan Tracey [hidden email]
Subject: Re: FW: [apollo] ORF viewer track

 

Not sure, doesn't Artemis also just show you the 6 frames and you can link the exons from them? Which functionally is similar to the 6-fame plugin.
I think last time I looked, only FMap did the whole Monty of frames, starts, stops, splice junctions and coding potential.

M

On 19/01/18 15:23, Faye Rodgers wrote:
Should I indeed.. ;)

 

I think what Alan wants is a view where you can see the whole gene (so not zoomed into the DNA track) with the all of the ORFs in the gene displayed (correct me if I’m wrong Alan). Does that exist?

 

 

From: Alan Tracey [hidden email]
Date: Friday, January 19, 2018 at 14:57
To: Faye Rodgers [hidden email]
Subject: Fwd: Re: [apollo] ORF viewer track

 

 


-------- Forwarded Message --------
Subject: 
Re: [apollo] ORF viewer track
Date: 
Fri, 19 Jan 2018 14:48:27 +0000
From: 
Michael Paulini [hidden email]
To: 
Alan Tracey [hidden email]
 
Hi Alan,

there is a plugin to show the 6 translation frames on the DNA track, Faye should know more about it.

Michael

On 19/01/18 14:46, Alan Tracey wrote:
Hi 


I'm working to annotate the Schistosoma mansoni genome.  I think Apollo could benefit from having a collapsible track to allow the viewing of ORFs.  Currently, I use Artemis in conjunction with Apollo to provide this missing information, but would love to be able to just use Apollo.  I really like using Apollo - it has some very nice functionality. 


Thanks, 

Alan 







 
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 
 
 
-- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
 


On 1/19/18 8:19 PM, Nathan Dunn wrote:

We have collapsible tracks (see below).  Not sure if this is what you meant, though.   

If you have a specific screenshot for the view you want, that would be helpful. 

Thanks, 

Nathan

<Screen Shot 2018-01-19 at 12.10.12 PM.png>


<Screen Shot 2018-01-19 at 12.10.04 PM copy.png>




On Jan 19, 2018, at 6:46 AM, Alan Tracey <[hidden email]> wrote:

Hi


I'm working to annotate the Schistosoma mansoni genome.  I think Apollo could benefit from having a collapsible track to allow the viewing of ORFs.  Currently, I use Artemis in conjunction with Apollo to provide this missing information, but would love to be able to just use Apollo.  I really like using Apollo - it has some very nice functionality.


Thanks,

Alan



-- 
The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. 



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 




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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 



-- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. 





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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