Hello Asha, The simpleRepeat track in the browser is based on Tandem Repeats Finder (TRF). The table/file behind the track can be extracted from the Table browser or downloaded.
If you want to BLAT in a way that completely ignores those regions, the hard-masked genomic reference sequence fasta would be the best choice. (But know that not all simpleRepeat/TRF items are masked as the masking is based on RepeatMasker plus only the simpleRepeat items with period of 12 or less). If you want to exclude all simpleRepeat items only, then use the utility maskOutFa program with a downloaded simpleRepeat.txt file (remove columns other than chrom, chromStart, chromEnd and name, and rename the file to .bed). Some help links: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Download http://genome.ucsc.edu/FAQ/FAQdownloads#download1 http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Asha Nair" <[email protected]> wrote: > From: "Asha Nair" <[email protected]> > To: [email protected] > Sent: Friday, January 29, 2010 1:27:44 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Locations on Human Genome for tandem arrays > > Hello, > > > > I am looking at human genome GRCh37 and trying to search for locations > on > the genome that have tandem arrays (repetitive elements) so that I > can > eliminate those regions for my statistical calculations. Could you > please > advice if there is a source on BLAT that gives this information, or > else how > I can find these regions using BLAT? > > > > Your help will be very much appreciated. > > > > Thanks and regards, > > > > Asha > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
