Hello, Using web tools, to perform a full intersection of the data from the RefSeq Genes track and the SNP track, the general method is to export both data sets to Galaxy (via the Table browser) and then use the function "Operate on Genomic Intervals -> Intersect".
To also include gene symbol information (it is not included in the RefSeq Gene track's primary table) you may wish to create a custom file (or track) based the UCSC Gene track instead. The UCSC Gene track contains RefSeq along with other input sources, concatenates the data down to a non-redundant set, and links in many types of common gene identifiers. This custom file could be used in entirety or filtered to only include those transcripts/genes that include input from RefSeq. Please examine the UCSC Gene track description page for the methods used. Then, using the Table browser, bring up the track and browse the associated tables using the "describe table schema" button. Once the desired table.fields are identified, select the output option of "selected fields from primary and related tables", format the result, and output to Galaxy. Here is some help for the Table browser that provides specific procedures and examples: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#SelectedFields http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#CustomTrack Help for Galaxy is also available through a mailing list and an FAQ from their web site. Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jing Hua Zhao" <[email protected]> wrote: > From: "Jing Hua Zhao" <[email protected]> > To: [email protected] > Sent: Friday, January 15, 2010 4:23:40 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] query over refGene and SNP information > > Dear Colleagues, > > > > I am trying to build a SNP-gene list, e.g., > > > > NM_018491 rs2260559 9 110676 CBWD1 CBWD1 COBW > domain containing 1 locus FOXD4 FOXD4 FOXD > > > > I am struggling with aligning information from refGene table with > snp126 > information but could not find an apparent way of doing this. > > > > I assume it could be done via refSeq but snp126 doesn't have it. Is > it > possible to do so? > > > > Many thanks in advance, > > > > > > > > Jing Hua Zhao > > > > MRC Epidemiology Unit, > Institute of Metabolic Science > Box 285 > Addenbrooke's Hospital, > Hills Road, Cambridge CB2 0QQ > United Kingdom > Tel: +44 (0)1223 769165 > email: [email protected] > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
