[Gmod-help] How to store sequence depth in Chado

[Scott Cain]

Hi Chris,

I'm ccing this to the schema mailing list to get input from other Chado users.

It sounds like the only information you want to store for the contig
is a number.  I would imagine that would most properly be a
featureprop.  While there is not a term for this in the
feature_property controlled vocabulary, you could easily add a term to
it like read_coverage.

If instead you want to add a density plot that would best be done with
wig data that could be stored external to the database with a property
that points to the file (that's the way it's done in GFF), or it could
be stored in the database proper, but I don't know where I'd put that
off hand.

Scott


On Thu, Apr 23, 2009 at 6:39 PM, Christopher Smith <smithcd at sfsu.edu> wrote:
> Hi,
>
> We are doing a genome project and have a bunch of 454 sequence reads that
> corresponds to genes.  We know the number of reads that goes into each
> contig (where the contig is all or part of a gene) and were wondering where
> read number/depth is stored in Chado.  Any ideas?
>
> Thanks,
> Chris
>
> ______________________________
> Christopher D. Smith Ph.D.
> Assistant Professor, Bioinformatics
> Department of Biology
> Center for Computing for Life Sciences
> San Francisco State University
> 1600 Holloway Ave.
> San Francisco, CA 94132
>
> smithcd at sfsu.edu
> office 415.405.2505
> office HH518
>
>



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