Hello Abigail, Using the table browser, sequence upstream or downstream of track features can be extracted and then saved into a custom track.
General path in Table browser: 1) select the starting track of interest (CpG Islands) 2) leave all default, except for setting region = genome\ 3) next set output as "custom track" click on "get output" 5) on the next form, "Create one BED record per:" set upstream or downstream bases and fill out the custom track information as desired. Save (your choice) then repeat for the other end (upstream of downstream). If the result are added to the browser (directly or later uploaded), they can be saved into a Session for later use, analysis in the Table browser, etc. Table browser help: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Custom tracks and Sessions: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Sessions Best wishes for your research project, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/19/10 9:37 AM, Farfan, Abigail wrote: > Dear Sir or Madam, > > In addition to searching for CpG islands in highly specific, balanced and > sensitive maps, is it possible to search specifically for CpG Islands Shores > in the USCS genome browser? > > If so, how do I get to that search function? > If not, do you have any other database recommendation, on CpG Island Shores > genome mapping information? > > The terms CpG Islands Shores was coined in the following references > (http://www.nature.com/ng/journal/v41/n2/full/ng.298.html and > http://www.nature.com/ng/journal/v41/n12/full/ng.471.html) where it was found > that most tissue-specific DNA methylation occurs in areas up to 2000 base > pairs distant from CpG islands. They have named these new sites CpG island > shores. > > Thank you for your advice. > > Abigail > > Abigail Farfan, M.A. > Roche NimbleGen > Phone: 608-218-7600, option #4 > Mail to [email protected] > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
