Hello, Yes, this can be done using the table browser. The positions will be those repeat annotations that overlap with your regions having coordinates anchored to the genomic reference sequence.
To do this, 1) Create a custom track (BED format) of your regions and save back to browser 2) Start with the RepeatMasker track and perform and intersection against the custom track 3) Download or save output back as another custom track. http://genome.ucsc.edu/cgi-bin/hgTables http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#SimpleIntersection http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks http://genome.ucsc.edu/FAQ/FAQformat#format1 To do a full join (and to link a specific entry from the RepeatMasker track with a specific entry from the custom track of coordinates), send both datasets to Galaxy and do a full join based on coordinate overlap (by checking Galaxy as the output option in the Table browser). The table rmsk (the primary table for the RepeatMasker track) contains the fields repName, repClass, and repFamily. For even more details, link out to the data's source at http://www.repeatmasker.org/ Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Lisa Olohan" <[email protected]> wrote: > From: "Lisa Olohan" <[email protected]> > To: [email protected] > Sent: Monday, January 11, 2010 2:20:00 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Repeat masker output > > Hello > I have a list of around 300 chromosomal locations in a text file in > the following format > chr3:100267-100367 > The list is composed of exons which contain repetitive sequences; is > > it possible to upload the file and obtain a list of where exactly the > > repetitive sequences are and a description of the type of repeats > assigned by repeat masker (e.g. SINE or microsatellite etc)? > Many thanks, > Lisa > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
