Hi Shibu, To retrieve the gene names you will need to use the table browser. To get to the table browser click on "Tables" in the navigation bar.
Select the "clade:", "genome:", and "assembly:" that you are interested in. Set group: "Gene and Gene Prediction Tracks" Set track: "UCSC Genes" Set table: "knownGene" Click on "define regions" You can either upload your list (the bed file) or paste it according to the instructions. Click on "Submit" Set output format: "selected fields from primary and related tables" If you would like to save it to a file, then specify a file name for output file: Click on "get output". Select the following: chrom, txStart, txEnd and geneSymbol (under the hg19.kgXref fields section) click on "get outPut" This should give you the data that you were looking for. Please contact the mailing list if you have further questions. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Shibu John" <[email protected]> To: [email protected] Sent: Tuesday, June 8, 2010 12:36:51 PM GMT -08:00 US/Canada Pacific Subject: [Genome] retrive gene names in BED format Hi, I have a BED file with 3 columns,.. ******* chr7 83772414 83772415 chr7 94937445 94937446 chr8 19819438 19819439 chr8 19819723 19819724 chr11 5248231 5248232 chr14 73683932 73683933 ******** I need to get the corresponding gene name in the fourth column.. ****************example.out********** chr7 83772414 83772415 SEMA3A chr7 94937445 94937446 PON1 chr8 19819438 19819439 LPL chr8 19819723 19819724 LPL chr11 5248231 5248232 HBB chr14 73683932 73683933 PSEN1 ****************** Is there any way to get this information from UCSC? Regards, Shibu John _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
