[BioC] SNP retrieval between two mouse strains

[Cook, Malcolm]

Sabrina,

I recommend you contact JAX with the specifics of you inquiry http://www.informatics.jax.org/software.shtml#sql

If you can avoid needing SQL access, by getting their help with your query, I would suggest that.

THat said, here is one source of summary info on ODBC drivers for Sybase: http://www.salmontraining.com/SybaseZone/articles/sybase_odbc_drivers_for_adaptive_server_enterprise.html 

I've not used any of them.  I was accessing under Unix and used FreeTDS.  I understand that FreeTDS can be used with ODBC on windows but is hard to build/configure - http://docs.moodle.org/en/Development:Compiling_FreeTDS_under_Windows

Good luck,

Malcolm Cook
Stowers Institute for Medical Research -  Bioinformatics
Kansas City, Missouri  USA
 
 

> -----Original Message-----
> From: sabrina [mailto:sabrina.shao at gmail.com] 
> Sent: Wednesday, March 30, 2011 10:14 AM
> To: Cook, Malcolm
> Cc: 'Hervé Pagès'; 'bioconductor at r-project.org'
> Subject: Re: [BioC] SNP retrieval between two mouse strains
> 
> Hi, Malcolm:
> Thanks for the information.
> I have been to the first website as for SNP query, but it did 
> not work because I have to specify a value for at least one 
> of the following
> fields: chr. Marker range or gene symbol, and I am after the 
> whole geneome
> 
> for the  SQL route, do I have to have SQL account if I use 
> RODBC? I never used that, can you show me what I need in 
> order to go that route? 
> I am using windows. Thanks
> 
> Sabrina
> 
> On 3/30/2011 6:52 AM, Cook, Malcolm wrote:
> > I think you'll find it at JAX using the form: 
> > http://www.informatics.jax.org/faq/STRN_SNP.shtml
> >
> > If you need it in a special format, or programmatic access, 
> they stored this in for in a Sybase relational database for 
> which you can request ( 
> http://www.informatics.jax.org/software.shtml#sql):
> > 	privs to connect
> > 	the database schema
> > 	assistance writing SQL to get out exactly what you need.
> >
> > If you go the SQL route, you will then want to access JAX 
> from within R and you would probably use RODBC with FreeTDS 
> based ODBC driver following 
> http://www.unixodbc.org/doc/FreeTDS.html.  I've done all but 
> the RODBC part and it works fine.
> >
> > Cheers,
> >
> > Malcolm Cook
> > Stowers Institute for Medical Research -  Bioinformatics 
> Kansas City, 
> > Missouri  USA
> >
> >
> >
> >> -----Original Message-----
> >> From: bioconductor-bounces at r-project.org
> >> [mailto:bioconductor-bounces at r-project.org] On Behalf Of 
> Hervé Pagès
> >> Sent: Tuesday, March 29, 2011 6:43 PM
> >> To: sabrina.shao at gmail.com
> >> Cc: bioconductor at r-project.org
> >> Subject: Re: [BioC] SNP retrieval between two mouse strains
> >>
> >> Hi Sabrina,
> >>
> >> On 03/29/2011 03:08 PM, sabrina wrote:
> >>> Dear list:
> >>> Is there anyway that I can retrieve genome-wide snp differences 
> >>> between A/J and C57BL/6J mouse strains, using any of the
> >> bioconductor packages?
> >>
> >> I don't think Bioconductor has any annotation package 
> containing this 
> >> information. Note that Bioconductor does not "produce" 
> annotations, 
> >> but re-packages/curates existing ones to make them more 
> convenient to 
> >> work with in the Bioconductor environment.
> >>
> >> In addition to those re-packaged annotations made available thru 
> >> hundreds of annotation packages, Bioconductor also 
> provides several 
> >> convenient tools for querying external resources like biomaRt (for 
> >> querying Ensembl and other BioMart services), rtracklayer for 
> >> downloading tracks from UCSC, and others...
> >>
> >> So more importantly than whether or not the information you are 
> >> looking for is available thru Bioconductor is the question 
> of whether 
> >> or not this information is available somewhere? Do you know any 
> >> external resource (Ensembl, UCSC, HapMap, dbSNP, etc...) 
> where this 
> >> information can be found?
> >>
> >> Note that the C57BL/6J strain is *the* reference genome for Mouse 
> >> (latest release is NCBI Build 37, also called mm9 by the 
> UCSC folks).
> >>
> >> H.
> >>
> >>
> >>> Thanks!
> >>>
> >>> Sabrina
> >>>
> >>> _______________________________________________
> >>> Bioconductor mailing list
> >>> Bioconductor at r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> Search the archives:
> >>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >> --
> >> Hervé Pagès
> >>
> >> Program in Computational Biology
> >> Division of Public Health Sciences
> >> Fred Hutchinson Cancer Research Center 1100 Fairview Ave. 
> N, M2-B876 
> >> P.O. Box 19024 Seattle, WA 98109-1024
> >>
> >> E-mail: hpages at fhcrc.org
> >> Phone:  (206) 667-5791
> >> Fax:    (206) 667-1319
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
>