Hi Vinodh, A complete set of the flat files used by our database is available through a web interface or ftp: http://hgdownload.cse.ucsc.edu/downloads.html ftp://hgdownload.cse.ucsc.edu/goldenPath/
To understand what data each file contains, the Table browser is very useful tool. Click on "Tables" in the top blue bar from any browser page or "Table browser" in the left blue bar on the gateway page here: http://genome.ucsc.edu/ Once here, you can drill down into the assemblies to data tracks and their individual tables. Use the "describe table schema" for an explanation of the contents. The table browser can also be used to create custom files containing only the data you are interested in (by selecting fields from the primary or related tables). Tracks that contain data about genes are in the group "Genes and Gene Prediction Tracks". UCSC Genes is the track with the most comprehensive set of linked data. The knownGene and linked kgAlias tables are a good place to start to gather the information you mention. It is also possible to create a custom track of your SNP data and use the Table browser to intersect it against one of the gene tracks to produce an output file with customized data fields. Here are some help pages to get you started: http://genome.ucsc.edu/FAQ/FAQdownloads#download31 http://genome.ucsc.edu/cgi-bin/hgTables#Help http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html http://genome.ucsc.edu/FAQ/FAQcustom Please ask if you need more help, Jennifer Jackson UCSC Genome Bioinformatics Group Vinodh Srinivasasainagendra wrote: > Hi, > > > > For a set of candidate SNPs (given their position and chromosome), I > would like to know what gene(s) the SNPs belong to. Can someone point me > to a file that contain all human genes along with their positional > information (gene-name, entrez gene id, coordinate, chrom ).? > > > > Thanks > > > > vinodh > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
