Dear Brook, Noted and thanks for your kindly help!
Regards, Tony 2012/5/19 Brooke Rhead <[email protected]> > 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<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<http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeV11> > > GENCODE Genes has "biotype" annotations (http://www.gencodegenes.org/** > gencode_biotypes.html <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 >> >> >> >> > -- * Sincerely, Tao Liu Li Ka Shing Institute of Health Sciences The Chinese University of Hong Kong Tel.+852-37636017 * _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
