questions about storing and viewing annotation files

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questions about storing and viewing annotation files

Richard Green
Hi GMOD users , I have a qucik questions I am working in a lab that is generating a lot of NGS (next generation sequencing data). I continously use annotation GFF files from UCSC , GENCODE, etc. I want to come up with a method to store and view these annotation. Maybe perform some basic stats on them. I setup one a DB inhouse running phpmyadmin, apache, mysql, and bioperl/perl. One of the requests I have received is to view junction data and look at Human ncRNA annotation. Any advice of suggestion has is muchly appreciated.
Thanks
-Rich

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Re: questions about storing and viewing annotation files

Scott Cain
Hi Rich,

The devel list is not nearly as populated as some of the other GMOD
lists, like for gbrowse ([hidden email]) and chado
([hidden email]), so it is possible that asking on
one of those lists will elicit more responses.

The question I have is if you can clarify a little more for me what
you want to do.  Let me see if I can restate and get it right: you
have ncRNA annotations (from somewhere, UCSC, NCBI, whatever), and
your researchers have come up with RNA-seq data (I'm inferring from
the "junction data"), and you'd like to display those "together" (and
possibly point out to the users where those things occur together).
Is that about right?

If I'm close, then GBrowse along with Bio::DB::Sam can take care of
the view question fairly straight forwardly.  There is an analysis
question (identifying when the two types of features occur together)
that GBrowse can't solve directly, but using BioPerl with the data
that is stored in either a database or Sam file for use with GBrowse
shouldn't be too hard to write in a one-off sort of way.

Scott


On Wed, Feb 2, 2011 at 2:13 PM, Richard Green <[hidden email]> wrote:

> Hi GMOD users , I have a qucik questions I am working in a lab that is
> generating a lot of NGS (next generation sequencing data). I continously use
> annotation GFF files from UCSC , GENCODE, etc. I want to come up with a
> method to store and view these annotation. Maybe perform some basic stats on
> them. I setup one a DB inhouse running phpmyadmin, apache, mysql, and
> bioperl/perl. One of the requests I have received is to view junction data
> and look at Human ncRNA annotation. Any advice of suggestion has is muchly
> appreciated.
> Thanks
> -Rich
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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