SNP retrieval between two mouse strains
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sabrina.shao ▴ 220
@sabrinashao-1661
Last seen 9.7 years ago
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? Thanks! Sabrina
SNP SNP • 1.3k views
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@herve-pages-1542
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Seattle, WA, United States
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
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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 >
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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
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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 > >
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The A/J genome was sequenced as part of the Sanger Mouse Genomes Project and you can obtain a list of SNPs they have called in tab- delimited format. http://www.sanger.ac.uk/resources/mouse/genomes/ The Mouse Phenome Database at JAX is also a great resource as they have merged SNPs from many projects and provide annotated lists. http://phenome.jax.org/ - Ben Benjamin L. King, M.S. Staff Scientist Mount Desert Island Biological Laboratory Salisbury Cove, ME 04672 On Mar 30, 2011, at 9:52 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@r-project.org >> [mailto:bioconductor-bounces@r-project.org] On Behalf Of Hervé Pagès >> Sent: Tuesday, March 29, 2011 6:43 PM >> To: sabrina.shao@gmail.com >> Cc: bioconductor@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@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@fhcrc.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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