extract non covered exons

[Maxime HEBRARD]

hello,
I try savant genome recently, and I want to extract specific data, so
I don't know if it is possible.

I have data from an exome capture of my individual.
I need to extract all the regions, whitch are annoted like "exon" on
RefGene DB, and are not covered more than 30X (for example)

Can I easily viewing thoses region on Savant or extract them to a
tabular file ?

Thanks for help

Maxime

[Eric J. M. Smith]

On 7 December 2011 09:14, Maxime HEBRARD <maxime....@gmail.com> wrote:
> I have data from an exome capture of my individual.
> I need to extract all the regions, whitch are annoted like "exon" on
> RefGene DB, and are not covered more than 30X (for example)
>
> Can I easily viewing thoses region on Savant or extract them to a
> tabular file ?

Hi Maxime,

Sorry, this is not the sort of thing that Savant does. Perhaps
somebody else in this group can suggest a tool for extracting this
information.

Sorry,

Eric Smith
Tarkvara Design Inc.

[Marc Fiume]

Alternatively, this is something that could easily be accomplished
through a plugin. Our API provides simple hooks for doing most of what
would be required for this computation. You could load your exon
regions as bookmarks, and the plugin could iterate through each of the
bookmarks, retrieve coverage information for a window, and add
bookmark descriptions (or generate some other report) denoting which
windows have no data.

Maxime, do you have experience with Java? We'd be happy to help
develop such a plugin.

Regards,
Marc

[Maxime HEBRARD]

Hi, I am experience with Java and I am interesting to develop a savant plugin.

I load amino acid demo in Eclipse

Can you tell me more about plugin development ?
How can y load exon position from refseq track ?

thx