CDS,UTR -> polypeptides in bulk GFF loader

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

CDS,UTR -> polypeptides in bulk GFF loader

Surya Saha
Hi Scott et al.,

This a question re the gmod gff3 bulk loader about how CDS/UTR features are handled. Is there a good reason why the polypeptide features are not named polypeptide:<gene name> in feature.uniquename? They are named auto<feature_id> by the loader.


Thanks

-Surya


--

Surya Saha
Sol Genomics Network, 
Boyce Thompson Institute, Ithaca, NY, USA.
Department of Plant Pathology, 
Cornell University, NY, USA.

------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: CDS,UTR -> polypeptides in bulk GFF loader

Robert Buels-2
I don't think there is a good reason.  polypeptide:<gene name> wouldn't
be good though, cause of multiple transcripts.

Probably want something more like polypeptide:<transcript name>


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/29/2014 08:00 AM, Surya Saha wrote:

> Hi Scott et al.,
>
> This a question re the gmod gff3 bulk loader about how CDS/UTR features
> are handled. Is there a good reason why the polypeptide features are not
> named polypeptide:<gene name> in feature.uniquename? They are named
> auto<feature_id> by the loader.
>
> See an example here https://gist.github.com/suryasaha/8690930
>
> Thanks
>
> -Surya
>
>
> --
>
> Surya Saha
> Sol Genomics Network,
> Boyce Thompson Institute, Ithaca, NY, USA.
> Department of Plant Pathology,
> Cornell University, NY, USA.
> http://www.linkedin.com/in/suryasaha
> Twitter: https://twitter.com/SahaSurya
>
>
> ------------------------------------------------------------------------------
> WatchGuard Dimension instantly turns raw network data into actionable
> security intelligence. It gives you real-time visual feedback on key
> security issues and trends.  Skip the complicated setup - simply import
> a virtual appliance and go from zero to informed in seconds.
> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>

------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema