Hello, The file is masked by both Tandem Repeats and Repeat Masker with specific settings. The readme document on the link you sent describes this. The Repeat Masker track in the Assembly database is slightly different.
One choice is to create a program yourself to extract all of the masked region coordinates. Or use one of our utilities (would require installing the code tree). This program would be a good choice: fakeOut: fake a RepeatMasker .out file based on a N's in .fa file http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities http://genome.ucsc.edu/FAQ/FAQdownloads#download27 thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Deniz Koellhofer" <[email protected]> wrote: > From: "Deniz Koellhofer" <[email protected]> > To: "genome" <[email protected]> > Sent: Tuesday, September 1, 2009 9:50:48 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] chromFaMasked masked sequence coordinates as BED file > > Hi, > > I was wondering if it possible to retrieve the coordinates masked out > in > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/chromFaMasked.tar > .gz as BED file. > > I've had a look at Tables > Variation and Repeats : RepeatMasker : > rmsk > and output format BED - however, this seems to include regions that > aren't masked out in chromFaMasked. > > Do I have to pick another track or is there another way to retrieve > this > information. > > Thanks for any help, > Deniz > > Deniz Koellhofer > Australian Genome Research Facility Ltd - > Bioinformatics > Level 5 Gehrmann Laboratories > Research Road > University of Queensland > St Lucia QLD 4072 > > ( +61 7 3346 7328 > 7 +61 7 3365 1823 > : [email protected]* > 8 www.agrf.org.au > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
