Hi Haojam, You are correct, the genomicCuperDups.txt file will provide you with genomic coordinates for segmental duplications. You can find more information by viewing the Segmental Dups track description page: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=genomicSuperDups. Clicking on "View table schema" will provide more details about the table itself. For transposable elements, I suggest rmsk.txt which is presented in the RepeatMasker track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=rmsk.
Let me also point out that you may search for tracks using our Track Search feature. From the Gateway page (http://genome.ucsc.edu/cgi-bin/hgGateway), choose your assembly and click the 'track search' button. Type in a search term (ex. segmental duplication) and click 'search'. For a description of the track, click on the track name. To turn on a track, click the checkbox next to the track and then click 'view in browser'. For more information about using Track Search, please refer to this help page: http://genome.ucsc.edu/goldenPath/help/trackSearch.html. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 3/8/2012 3:23 AM, 하오잠 로 wrote: > UCSC Group > > Dear Sir/Miss, > I would like to retrieve segmental duplication and transposition or > transposable element genomic coordinates stating chromosome positions from > UCSC genome browser for human genome reference hg18. I have located > genomicSuperDups.txt and transMapAlnRefSeq.txt at the UCSC ftp site. Is these > files mean for segmental duplication and transposition respectively. I would > be glad and highly appreciate for your kindness. > > Regards, > Haojam Rocky > > ===================================== > Seoul National University Biomedical Informatics (SNUBI), > Div. of Biomedical Informatics, > Seoul National University College of Medicine > Ph.D. Candidate, Haojam Rocky > Phone) +82-2-740-8319 > ===================================== > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
