Hi Zhi, You can create a custom track of the upstream regions and a custom track of your SNPs and use the Table Browser to intersect them. If you are unfamiliar with these tools, some helpful information is here:
http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28 and http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser Create the upstream custom track by selecting the FlyBase Genes track in the Table Browser (or one of the other gene tracks, if you prefer), then make sure "region: genome" is selected and choose "output format: custom track." Hit "get output." On the next page, name your track something like "upstream" and select the button to create one BED record per "upstream by 5000 bases." Hit the "get custom track in genome browser" button and make sure it created a track that is the regions you want. Next, hit the "manage custom tracks" button under the main Genome Browser display, and choose to add a custom track. It is likely that you will want to use BED format (http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED). Once you have both of your custom tracks, select the SNP track in the Table Browser, hit "intersection: create" and select the upstream custom track, and then back on the main Table Browser page choose the output format you want and hit "get output." You should have a list (or a custom track) of the SNPs that are in the upstream regions of genes in dm3. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/7/11 1:11 PM, Zhi Zhang wrote: > Hi, All, I have some SNP position data in dm3 and want to find > whether they are in 5kb upstream region in dm3 genome. how can I do > that in table search of UCSC? > > THANKS > > > > > Zhi Zhang, Ph. D. Sanford-Burnham Medical Research Institute 10901 > North Torrey Pines Rd. La Jolla, CA 92037, USA Phone 858-646-3100 > ext. 3801 Fax 858-795-5298 > > > _______________________________________________ Genome maillist - > [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
