Good Afternoon Dana:
You could produce such a list from a given position with a MySQL operation to the UCSC public MySQL server. Note this Wiki page with a description of the command:
http://genomewiki.ucsc.edu/index.php/Finding_nearby_genes
--Hiram
----- Original Message ----- From: "Dana Levasseur" dana-levasseur@uiowa.edu To: galaxy-user@lists.bx.psu.edu Sent: Wednesday, August 25, 2010 3:26:28 PM GMT -08:00 US/Canada Pacific Subject: [galaxy-user] FW: [Genome] Genome-wide dataset of protein location conversion
Hello,
We have been trying to determine a method to convert ChIP-Seq coordinates into a list of genes and are wondering the best way to utilize the Galaxy browser. The UCSC folks suggested you could help but I should have been more specific with my request. Ideally we would like to take global binding coordinates and find out what genes are nearby (ie at either a 1 or 5kb) instead of simply the “closest feature”. Might you be able to advise on this? I have enclosed the text (.bed format) file I used to get the binding sites in the UCSC genome browser. Thanks in advance!
Cheers,
Dana