[Gmod-ajax] Extract NT Sequence By Coordinates?

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[Gmod-ajax] Extract NT Sequence By Coordinates?

Ben Bimber
Hello,

JBrowse is proving to be a pretty useful tool for users; however, there's one question I get a lot.  People are looking over a region, and they want to extract the NT sequence of the reference over that region.  Is there a built in way to do this?  

If you view the details on most features, it shows NT sequence; however, that only works if there is a feature.  I would think this would be an option under the main menu or perhaps connected to the NT track.

Thanks,
Ben

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Re: Extract NT Sequence By Coordinates?

dmgood11
Assuming the Reference Sequence track is active, you can right click on the track label, select "Save Track Data", and grab the reference sequence corresponding to the visible region, independent of the presence of features.  See the attached Phytozome JBrowse screenshot as an example.

-David

On Fri, Aug 26, 2016 at 8:56 AM, Ben Bimber <[hidden email]> wrote:
Hello,

JBrowse is proving to be a pretty useful tool for users; however, there's one question I get a lot.  People are looking over a region, and they want to extract the NT sequence of the reference over that region.  Is there a built in way to do this?  

If you view the details on most features, it shows NT sequence; however, that only works if there is a feature.  I would think this would be an option under the main menu or perhaps connected to the NT track.

Thanks,
Ben

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David M. Goodstein, Ph.D.
Phytozome Group Lead
Eukaryotic Data Systems
Joint Genome Institute - U.S. Dept. of Energy


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Screen Shot 2016-08-26 at 11.50.40 AM.png (864K) Download Attachment
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Re: Extract NT Sequence By Coordinates?

Ben Bimber
i figured i was missing something - thanks.

On Fri, Aug 26, 2016 at 11:51 AM, David Goodstein <[hidden email]> wrote:
Assuming the Reference Sequence track is active, you can right click on the track label, select "Save Track Data", and grab the reference sequence corresponding to the visible region, independent of the presence of features.  See the attached Phytozome JBrowse screenshot as an example.

-David

On Fri, Aug 26, 2016 at 8:56 AM, Ben Bimber <[hidden email]> wrote:
Hello,

JBrowse is proving to be a pretty useful tool for users; however, there's one question I get a lot.  People are looking over a region, and they want to extract the NT sequence of the reference over that region.  Is there a built in way to do this?  

If you view the details on most features, it shows NT sequence; however, that only works if there is a feature.  I would think this would be an option under the main menu or perhaps connected to the NT track.

Thanks,
Ben

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David M. Goodstein, Ph.D.
Phytozome Group Lead
Eukaryotic Data Systems
Joint Genome Institute - U.S. Dept. of Energy



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Re: Extract NT Sequence By Coordinates?

Colin
You can also export the sequence from a highlighted region using "Save track data" too. The option to export the highlighted region appears in the "Save track data" dialog if a highlight exists, which could be more precise than visible region


-Colin

On Fri, Aug 26, 2016 at 1:52 PM, Ben Bimber <[hidden email]> wrote:
i figured i was missing something - thanks.

On Fri, Aug 26, 2016 at 11:51 AM, David Goodstein <[hidden email]> wrote:
Assuming the Reference Sequence track is active, you can right click on the track label, select "Save Track Data", and grab the reference sequence corresponding to the visible region, independent of the presence of features.  See the attached Phytozome JBrowse screenshot as an example.

-David

On Fri, Aug 26, 2016 at 8:56 AM, Ben Bimber <[hidden email]> wrote:
Hello,

JBrowse is proving to be a pretty useful tool for users; however, there's one question I get a lot.  People are looking over a region, and they want to extract the NT sequence of the reference over that region.  Is there a built in way to do this?  

If you view the details on most features, it shows NT sequence; however, that only works if there is a feature.  I would think this would be an option under the main menu or perhaps connected to the NT track.

Thanks,
Ben

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David M. Goodstein, Ph.D.
Phytozome Group Lead
Eukaryotic Data Systems
Joint Genome Institute - U.S. Dept. of Energy



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