Hi, Thank you very, very much for your help.
Thanks, Wailoon -----Original Message----- From: Jennifer Jackson [mailto:[email protected]] Sent: Tuesday, November 24, 2009 5:04 AM To: ONG Wai Loon Cc: [email protected] Subject: Re: [Genome] self chain database block information Hello, The version of the data as contained in the main mySQL database does not contain the detailed information of the alignment. Instead, you will want to access the chain file on Downloads. For hg18, this is located here: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsSelf The data format is described here: http://genome.ucsc.edu/goldenPath/help/chain.html In general, for the same data for any assembly (when it exists), go to: http://hgdownload.cse.ucsc.edu/ , then navigate to the data like this: Downloads -> common name -> assembly version -> Pairwise Alignments -> "Common name" self alignments Ftp the data and use your own tools for analysis. There are some utilities in the kent source tree that may be interesting to you. This is a list of all utilities, search for the work "chain" to locate those that manipulate chain data (some are for the mySQL database, others work with the flat files). http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities And here is a link with instructions for obtaining the source. README files throughout the download contain technical instructions and other usage information: http://genome.ucsc.edu/FAQ/FAQdownloads#download27 Please let us know if you need additional help, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "ONG Wai Loon" <[email protected]> wrote: > From: "ONG Wai Loon" <[email protected]> > To: [email protected] > Sent: Sunday, November 22, 2009 7:17:00 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] self chain database block information > > Hi, > > I'm working on a project involving the use of the self chain > databases > (chr*_chainSelf), and through the browser I see that aligning blocks > exists within the self chain, together with deletions represented by > a > single line and other features. However, the database gives only > information on the entire self chain region and I couldn't find > anything > that shows the locations of those aligning blocks. Is it possible to > teach me how I can extract those block information from the self > chain > databases? Thank you very much for the trouble taken. > > Thanks, > Wailoon > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
