Feature Sequence

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Feature Sequence

Saari, Travis

Hi all,

 

I posted the following issue to the github page: https://github.com/GMOD/jbrowse/issues/659 and was instructed by Nathan to send an e-mail to you all to see if something like this was possible.

 

My goal is to have an export function for the sequence of a feature, for instance a predicted gene. In In Apollo, the annotation tracks have this functionality. I would like to do the same thing for non-annotation tracks, and preferably within JBrowse itself as I do not have an Apollo instance running on a server yet.

 

Thanks,

 

Travis Saari

Student Services Contractor at

US-EPA

Mid-Continent Ecology Division

218. 529.5178

 

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Re: [Gmod-ajax] Feature Sequence

Ian Holmes-2
Hi Travis,
The JBrowse/Store/SeqFeature object has a getReferenceSequence method that returns the reference sequence for a given feature. This is used by JBrowse/View/Track/_FeatureDetailMixin to implement the "Region sequence" field in the feature default window that you get by right-clicking on a feature (in an HTMLFeatures or CanvasFeatures track) and selecting "View details". Since JBrowse does not currently have a way of selecting a feature per se (just highlighting a region of sequence), I'm not sure exactly how you want this feature to look in JBrowse, but it should be possible. I suspect someone in the community may even have done it but I'm not sure.
Cheers,
Ian

On Mon, Nov 23, 2015 at 11:55 AM, Saari, Travis <[hidden email]> wrote:

Hi all,

 

I posted the following issue to the github page: https://github.com/GMOD/jbrowse/issues/659 and was instructed by Nathan to send an e-mail to you all to see if something like this was possible.

 

My goal is to have an export function for the sequence of a feature, for instance a predicted gene. In In Apollo, the annotation tracks have this functionality. I would like to do the same thing for non-annotation tracks, and preferably within JBrowse itself as I do not have an Apollo instance running on a server yet.

 

Thanks,

 

Travis Saari

Student Services Contractor at

US-EPA

Mid-Continent Ecology Division

<a href="tel:218.%20529.5178" value="+12185295178" target="_blank">218. 529.5178

 


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