[Gmod-help] massively parallel sequencing question

[Scott Cain]

Hi Jennifer,

I'm cc'ing the GMOD schema mailing list, because there have been other
people wondering the same thing.

First I should say that I don't really know, because no one has tried
it.  That said, I can tell you that the FlyBase Chado schema has several
million rows in their feature table and it works for them.  What you no
doubt would need is a database server with enough horsepower and memory
to do the job, as well as properly tuning the database server for
performance.

For use with GBrowse, I don't think I would advocate using Chado
directly, as the Chado adaptor for GBrowse is significantly slower than
the Bio::SeqFeature::Store database which is designed specifically for
giving speedy query results for use with GBrowse.  You could set up a
system where you use Chado as your working/annotation database and then
set up a periodic dump of your features to GFF3 which would get loaded
into a SeqFeature::Store database for use with GBrowse.

Also, in the upcoming release of GBrowse there will be support for
wiggle tracks like in the UCSC browser, which will be well suited for
displaying things like coverage density in a fast-rendering way.

Scott


On Thu, 2008-05-29 at 08:38 -0600, Jennifer Beane wrote:
> Hi,
>  
> I'm a post-doctoral fellow in bioinformatics and my lab is about to
> receive data generated from a massively parallel sequencing platform
> --  Illumina's genome analyzer.  The data will contain several million
> short sequence reads from mRNA and microRNA.  There are several
> software packages to align the reads to the human genome, but I will
> need to create a way to store, filter, and efficiently annotate these
> reads.  I'm thinking of loading the data into a chado database, and
> using applications such as GBrowse to view the data.  I'm wondering if
> you have any experience with using GMOD software/applications for this
> type of data?  I'm wondering if the data will be too extensive to be
> queried in a database?  If you have any advice/suggestions I would
> really appreciate it.
>  
> Thank you very much,
> Jennifer Beane, Ph.D
> Post-doctoral Fellow
> Boston University School of Medicine
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory