UCSC genome browser mm39 displays repeitive elements called by repeatmasker (tracks for LINE, SINE, LTR, satellites... etc). Unfortunately, the repeatmasker website only has downloads up to mm10. Presumably UCSC ran repearmasker themselves. Is there anywhere I can download these tracks?
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saarantras •
Hello,
We did run repeat masker in house (https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm39&c=chr12&g=rmsk). The data can be modified/extracted using the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) or you can also use our API for programmatic access (http://genome.ucsc.edu/goldenPath/help/api.html).
The entire track data file can be found in our download server: http://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/rmsk.txt.gz
If you have any follow up questions, our public help desk can always be reached at genome@soe.ucsc.edu. You may also send questions to genome-www@soe.ucsc.edu if they contain sensitive data. For any Genome Browser questions on Biostars, the UCSC tag is the best way to ensure visibility by the team.
Can I know how do you generate this file? For example, what's the version of Dfam and RepeatMasker used?
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where did you find mm36 ?
http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm36
Whoops, I meant to type "39", not 36.