Hello, The program is in the kent source tree location: kent/src/hg/maskOutFa http://genome.ucsc.edu/FAQ/FAQdownloads#download27
And yes, the file simpleRepeat.txt is the primary table for the track simpleRepeat. Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Asha Nair" <[email protected]> wrote: > From: "Asha Nair" <[email protected]> > To: "Jennifer Jackson" <[email protected]> > Cc: [email protected] > Sent: Monday, February 1, 2010 9:38:27 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Locations on Human Genome for tandem arrays > > 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
