Hi Atteeq, There are two tables related to UCSC Genes that you can use to get a single splice variant for each gene: knownCanonical and knownIsoforms. The knownIsoforms table contains all the items in knownGene grouped into clusters, and knownCanonical contains contains a single isoform for each cluster, along with it's position. For more information on how these tables are made, please see: https://lists.soe.ucsc.edu/pipermail/genome/2005-July/008123.html
Using the Table Browser, select a clade, genome, and assembly of your choice, then make the following selections: group: Genes and Gene Prediction Tracks track UCSC Genes table: knownCanonical region: genome identifiers: paste in a list or upload a file containing your genes of interest output format: BED - browser extensible data output file: enter a file name to save your results to a file, or leave blank to display results in the browser Click 'get output'. On the following page, select any additional options then click 'getBED'. I hope this helps answer your question. Please contact us again at [email protected] if you have additional questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 10/4/2011 1:08 PM, Rehman, Atteeq (NIH/NIDCD) [F] wrote: > Hi, > > I would like to get a bed file containing gene identifier number and > coordinates of all the coding exons of my genes of interest (approximately > 100 genes). I tried to accomplish this by using the table option in the UCSC > genome browser but there is a problem. Say a gene X has 4 splice variants so > using table option from UCSC genome browser will give me four sets of coding > exons, one set of exons for each splice variant. Is it possible to get only > one set of coding exons containing merged exons from all splice variants? I > can merge exons using Galaxy but then I will lose the gene identifier number, > which I don't want. Thanks a lot for your help > > Best Regards, > Atteeq > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
