Hi Dean, Yes, just use the table browser (http://genome.ucsc.edu/cgi-bin/hgTables).
Select the gene set you want to compare against (e.g., track UCSC Genes, table knownGene) and then create an intersection with your bed file that you've uploaded as a custom track. On the "create intersection page" choose the option (using UCSC Genes as an example): • "All UCSC Genes records that have no overlap with [CustomTrackName]" - or even - • "All UCSC Genes records that have at most [ x ]% overlap with [CustomTrackName]" ... Click submit there and just choose what output format you want. - Greg On 11/2/11 3:06 PM, Dean Phelan wrote: > Hi Greg, > > Sorry I wasn't clear. I have a bed file from an exome capture, I > imported it into UCSC to compare the captured region to the gene > annotation track to identify regions not covered by the exome capture. > I can do this visually but was wondering if there was a way of quickly > retrieving genes that are not captured. > > Hope this makes sense. > > Thanks > Dean > > > -----Original Message----- > From: Greg Roe [mailto:[email protected]] > Sent: Wednesday, 2 November 2011 9:33 AM > To: Dean Phelan > Cc: [email protected] > Subject: Re: [Genome] Bed files > > Hi Dean, > > BED files do not contain sequence to compare against a genome, so I'm > unsure of what you're asking for. Perhaps you're wanting to compare a > bed file with a gene annotation track? > > Can you clarify your question a bit more? > > Thanks! > > - Greg > > > On 10/30/11 11:01 PM, Dean Phelan wrote: >> Hi, >> >> >> >> Is there a way I can use the UCSC genome browser to compare a bed file >> to the latest genome assembly and get a list of regions that differ? >> >> >> >> Thanks for your help. >> >> >> >> Dean >> >> >> >> >> ______________________________________________________________________ >> This email has been scanned by the MessageLabs Email Security System. >> For more information please visithttp://www.messagelabs.com/email >> ______________________________________________________________________ >> _______________________________________________ >> Genome maillist [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > > If you have any question, please contact MCRI IT Helpdesk for further > assistance. > ______________________________________________________________________ > > ______________________________________________________________________ > This email has been scanned by the MessageLabs Email Security System. > For more information please visit http://www.messagelabs.com/email > ______________________________________________________________________ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
