Hi Nicolas, If you are trying to find the nearest Ensembl Gene to a set of coordinates you will first have to create a custom BED track of your pseudogene coordinates (http://genome.ucsc.edu/goldenPath/help/customTrack.html). After you have displayed your custom annotation track, go to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) and, making sure your table is selected, click on the "Send output to Galaxy" box and then "get output". After your track has loaded at Galaxy, go back to the Table Browser and select the Ensembl Genes track (in Genes and Gene Prediction Tracks) and export this table as well to Galaxy. Galaxy has a tool called " Fetch closest feature" under "Operate on Genomic Intervals" that should be able to help you. If you have questions about Galaxy, please contact their help desk at [email protected].
I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 9/15/10 4:08 PM, Vanessa Kirkup Swing wrote: > Hi Nicolas, > > The Table Browser would help you with this. To get to the Table Browser click > on the "Tables" link on the blue navigation bar. > > You will need to set the following clade, genome, assembly drop downs. > > You will need to also set the following: > group: Genes and Gene Prediction Tracks > track: Ensembl Genes > table: ensGene > region: position (put in the coordinates of the pseudogene and the area > around it that you are interested in) > output format: selected fields from primary and related tables > output file: put in a fileName if you would like to save the output to your > computer > > Click on "get output" > > Select the items that you would like to have displayed in your output. You > will want to select "name" to output the ensembl id. > > Click on "get output". > > Hope this helps. Please don't hesitate to contact the mailing list again if > you have further questions. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ----- Original Message ----- > From: "Nicholas Price"<[email protected]> > To: [email protected] > Sent: Tuesday, September 14, 2010 11:23:35 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Question > > Hi, > > I have the coordinates of a pseudogene and I want to locate the genes on > either side of the pseudogene. As output I will like the ensembl gene IDs > > Thanks you > > Nicholas > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
