Get sequence with exons/introns marked

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Get sequence with exons/introns marked

Alan Tracey
Hi


I want to get sequence for my gene, including the introns. Currently, I
can see that 'genomic sequence' gives me this, but it would be really
nice to have the introns/exons highlighted - maybe lower case for
introns and upper for exons?


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: Get sequence with exons/introns marked

nathandunn

I think that is a great feature that a lot of other sequence viewers have and I would like JBrowse / Apollo to have.  

Can you create an issue, potentially with a screenshot that represents what you want it to look like if you have one.   Otherwise, I think your text description makes sense.


Thanks,

Nathan

On Jan 22, 2018, at 5:34 AM, Alan Tracey <[hidden email]> wrote:

Hi


I want to get sequence for my gene, including the introns. Currently, I can see that 'genomic sequence' gives me this, but it would be really nice to have the introns/exons highlighted - maybe lower case for introns and upper for exons?


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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Re: Get sequence with exons/introns marked

Deepak Unni
There already exists two plugins for JBrowse that does this:


It would be awesome to have something like this for Apollo's sequence export.


On Mon, Jan 22, 2018 at 11:29 AM, Nathan Dunn <[hidden email]> wrote:

I think that is a great feature that a lot of other sequence viewers have and I would like JBrowse / Apollo to have.  

Can you create an issue, potentially with a screenshot that represents what you want it to look like if you have one.   Otherwise, I think your text description makes sense.


Thanks,

Nathan

On Jan 22, 2018, at 5:34 AM, Alan Tracey <[hidden email]> wrote:

Hi


I want to get sequence for my gene, including the introns. Currently, I can see that 'genomic sequence' gives me this, but it would be really nice to have the introns/exons highlighted - maybe lower case for introns and upper for exons?


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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--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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Re: Get sequence with exons/introns marked

nathandunn

Thanks.  Alan created an issue here: https://github.com/GMOD/Apollo/issues/1854

I added those links there.  I think it uses a pretty similar code-base, so hopefully we can port that forward into Apollo.    We have a bit of a backlog for other stuff if someone wants to take a shot at it, though. 


On Jan 22, 2018, at 10:34 AM, Deepak Unni <[hidden email]> wrote:

There already exists two plugins for JBrowse that does this:


It would be awesome to have something like this for Apollo's sequence export.


On Mon, Jan 22, 2018 at 11:29 AM, Nathan Dunn <[hidden email]> wrote:

I think that is a great feature that a lot of other sequence viewers have and I would like JBrowse / Apollo to have.  

Can you create an issue, potentially with a screenshot that represents what you want it to look like if you have one.   Otherwise, I think your text description makes sense.


Thanks,

Nathan

On Jan 22, 2018, at 5:34 AM, Alan Tracey <[hidden email]> wrote:

Hi


I want to get sequence for my gene, including the introns. Currently, I can see that 'genomic sequence' gives me this, but it would be really nice to have the introns/exons highlighted - maybe lower case for introns and upper for exons?


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.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



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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