Hi Mike, You can get information in batch from the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables). Select the clade, genome and assembly that you want to use, and then:
group: Genes and Gene Prediction Tracks track: choose the gene track you want to use. (When you paste a gene name into the position/search box, several tracks at once are searched, but you need to pick one specifically in the Table Browser.) To see how any of the gene tracks were created, hit the "describe table schema" button and scroll down. region: genome identifiers: this is where you can paste or upload your list of genes output format: I would choose either "all fields from selected table" or "BED format" A few things to be aware of: - You can either start from the Genome Browser and check the "send ouput to Galaxy box", or start from Galaxy, which takes you to the Table Browser when you click on "get data" and then "UCSC Main table browser". - If you are using gene symbols, you will likely get more than one transcript for each gene. If you only want a single representative gene for each cluster of transcripts and you want to use the UCSC Genes set, you can use the "knownCanonical" table. - SNPs that are insertions may not show up in an intersection, as they do not take up any room on the reference genome. Hope this helps! If you have more questions for UCSC, please contact us again at [email protected]. If you have questions for Galaxy, their helpdesk address is [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group Gonzalez, Michael A (Research Adm) wrote on 10/4/10 2:15 PM: > To whom it may concern: > > I know that if I use the genomes tab and enter a specific gene name > it will give me the chromosome location and the start and end position of that gene. I was wondering if there was a way to submit a long list of genes and have the browser give me all the position information for the whole list at once? The goal is to have galaxy run an intersect of these genes with dbSNP131 and count the number of known SNPs on a given gene. I would greatly appreciate the help! > > Thanks, > > Mike G > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
