Thank you Jennifer. This helps me a lot. How do I get to the utility maskOutFa program from BLAT? The downloaded simpleRepeat.txt file that you have mentioned would be the file with all the tandem repeats for the whole genome/or a specific region on the genome that I would get from simpleRepeat track right?
Thanks again! Asha On Fri, Jan 29, 2010 at 7:21 PM, Jennifer Jackson <[email protected]> wrote: > 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
