Hi Tony, For future reference, the "Track Search" tool (which you can get to by hitting the "track search" button under the main Genome Browser graphic on http://genome.ucsc.edu/cgi-bin/hgTracks) is a good place to start looking for data tracks that are relevant to you. If you enter "rRNA" into the search box, several tracks are suggested, and you can click on the links in the track name column to read descriptions of the tracks and see if any are what you are looking for.
I suggest using the GENCODE Genes track, which you can read about here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeV11 GENCODE Genes has "biotype" annotations (http://www.gencodegenes.org/gencode_biotypes.html) that can be used to filter the set so that you get only the rRNA genes. To do this, go to GRCh37/hg19 in the Table Browser and select: group: Genes and Gene Prediction Tracks track: GENCODE Genes V11 table: Basic (wgEncodeGencodeBasicV11) region: genome output format: BED Now hit the "filter: create" button. On the next page, scroll down and check the box next to hg19.wgEncodeGencodeAttrsV11 and hit "allow filtering using fields in checked tables". Add a filter so that "transcriptType does match rRNA" and hit submit. Then hit "get output" and "get BED". The result should be 531 rRNA transcripts from the GENCODE Genes track in BED format. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 5/17/12 9:33 PM, Tony wrote: > Dear Steve, > > Sorry for trouble you. > > I would like to know how to download rRNA bed file from UCSC. I try to find > the file on UCSC tables section, but I can not find it out. Would you > please show me some hints? > > Regards, > Tony > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
