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

[Christopher Smith]

Scott,

Thanks, as always, for the speedy response.  Yes, we just want to  
capture that, for example, 112 reads went into assembling a given  
contig.  It is just a single number and we only want to capture the  
read depth at the level of the contig, not a sliding window across the  
contig.

We thought of adding to the feature_prop.  Usually I tend to make a  
best guess and insert where I think it should go, but was making an  
effort to see if there was a standard yet. We have a transcriptome so  
a WIG plot is not quite what we need yet.

Thanks again, we'll use the feature_prop suggestion unless something  
else shows up in the thread.

Have a nice weekend,
Chris


On Apr 23, 2009, at 7:59 PM, Scott Cain wrote:

> 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

______________________________
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