Hi Satya, If you are looking for the nearest gene to a genomic coordinate, you should use Galaxy ( http://main.g2.bx.psu.edu/). Load your coordinates as a custom track on the UCSC genome browser, go to the table browser and send the output to Galaxy (click the check box after the output option pull down menu). I believe the tool you want is "Fetch closest feature" under the "Operate on Genomic Intervals" menu. If you have questions about Galaxy, please contact their help desk at [email protected] <mailto:[email protected]>.
I hope this information addresses your question and is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 8/11/10 10:03 PM, Das, Satyabrata wrote: > Hello, > > > I am analyzing a genome-wide dataset of protein location coordinates in the > following format and want to know if they can be converted to the gene that > they are most closely located next to: > > > chr1:3002834-3002851 > chr1:4132776-4132783 > chr1:4322743-4322748 > chr2:155204062-155204080 > chr2:155207569-155207570 > chr2:155209754-155209758 > chr2:155275773-155275774 > chr2:155311478-155311484 > > > The coordinates are derived from the mm8, Feb 2006, Build 36 genome build. I > would like to know if the UCSC table browser has a batch function that > enables conversion of these coordinates into the gene descriptions or gene > symbols that the binding sites are positioned near (either within the gene > bodies or intergenically). > > > > Thank you, > Satya > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
