Hello Mike, Details for how repeatmasker is run for any genome can be found on the Repeatmasker description page (click on the track name in the browser) and is documented here:
http://genome.ucsc.edu/FAQ/FAQdownloads#download16 With the specific area on downloads here: http://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/ chromOut.tar.gz - RepeatMasker .out files (one file per chromosome). RepeatMasker was run with the -s (sensitive) setting. May 17 2007 (open-3-1-8) version of RepeatMasker, Repeat Masker library RELEASE 20061006 Going out to the repeatmasker http://www.repeatmasker.org. or Repbase http://www.girinst.org/repbase/update/index.html web sites can help you to understand the contents of the various libraries. Some do contain mixed-species content, as you have noticed. If you still need help, please feel free to contact the mailing list support team again for more assistance. Warm regards, Jen UCSC Genome Browser Support On 8/31/10 7:25 AM, Michael Muratet wrote: > Greetings > > I downloaded the rmsk file for mouse from the UCSC Genome Browser in > BED format to check for repeats in RNA-seq data I have. One of the > matches was LSU-rRNA_Hsa and I realized yesterday that Hsa probably > means Homo sapiens. The track shows up in the browser for mm9, e.g., > chr1:7765877-7765933, and I assume that the human sequence was used to > search the mouse genome to generate the mask file. Is this a correct > assumption? > > Thanks > > Mike > > Michael Muratet, Ph.D. > Senior Scientist > HudsonAlpha Institute for Biotechnology > [email protected] > (256) 327-0473 (p) > (256) 327-0966 (f) > > Room 4005 > 601 Genome Way > Huntsville, Alabama 35806 > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
