Hello, Cathy. You can do this by using our Table Browser. If you're unfamiliar with the Table Browser, please see the User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
I did not find any items matching SAT1 in the RepeatMasker track, but there is a class called "Satellite." In the Satellite class, I did find some items named RNSAT1. If this is not what you had in mind, if you find a result in the Browser that does match what you're looking for, you can enter that result into the Table Browser (in step 4 below). For now, let's assume you're looking for RNSAT1 in the following example: 1. From http://genome.ucsc.edu, select "Tables" from the blue navigation bar at the top of the screen. 2. Select the following options: Clade: Mammal Genome: Rat Assembly: Nov. 2004 (Baylor 3.4/rn4) Group: Variation and Repeats Track: RepeatMasker Table: rmsk Region: Select either "genome" for the entire genome or specify a region next to "position" 3. Next to "filter," click the "create" button 4. The "repName" line should read: repName does match RNSAT1 5. Click the "submit" button 6. Click the "get output" button You can adjust step 4 based on whether you want to search for an entire class or family of repeats or a specific repeat name. You can also use wildcards such as SAT* or *SAT* if you're not sure of the name or if you want to include multiple results with similar names. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Cathy Cummings-Lorbetskie Sent: Wednesday, January 11, 2012 10:24 AM To: [email protected] Subject: [Genome] How to question - downloading repeated element tracks from rat genome Hello, I have a "how to" question regarding UCSC genome data . The assembly I am interested is Rat (RN4 v3.4) and the annotation is SAT1 (repeat masker track). I have tried without suceeding to extract the Satellite alpha I repeated sequences as described in the published paper, Hamm CA et al 2009. On page 3 (of their .pdf) Hamm et al describe the following: "Rat genome sequence (rn4/version 3.4, Nov. 2004) and the annotation for repetitive elements were obtained from the UCSC Genome Database. Based on genomic co-ordinates of LINE elements provided by the UCSC database, 899,092 LINE sequences were extracted" Thank you in advance for any help with this. Cathy Cummings-Lorbetskie ____________________________________________ HECSB / DGSECC Hazard Identification Division Health Canada / Santé Canada Ottawa, ON K1A 0K9 AL / IL: 0803B Tel: 613-954-7140 Fax: 613-948-9413 E-mail: [email protected] _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
