Downloading H. sapiens rRNA coordinates

[Alexandra Dana]

Hi 

I'm trying to download H. sapiens rRNA coordinates, but I did not find an entry in table browser wizard that enables me to select such field (e.g. the 'track' dropbox).

Is it possible to download such an annotation of the genes?

Thanks in advance, 

Alexandra

[Matthew Speir]

Hello Alexandra,

Thank you for your question about retrieving rRNA coordinates. Our GENCODE Genes V17 track for hg19 does contain rRNA genes and their coordinates, as well as a small set of other ncRNA families. For more information on this track please refer to the track description page: http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeGencodeV17. This information can be retrieved using the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables). Use the following to access this information:

clade: Mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions Tracks
track: GENCODE Genes V17
table: Basic (wgEncodeGencodeBasicV17)
output: BED - browser extensible data

Click 'Filter'. Select the wgEncodeGencodeAttrsV17 from the 'Linked Tables' section and click 'allow filtering using fields in checked tables'. After the page refreshes, type rRNA in the 'transciptType' field of the hg19.wgEncodeGencodeAttrsV17 based filters section. Then click 'submit'.

After you return to the main Table Browser page, click 'get output'.

For more information on how to use the Table Browser, please refer to our help pages:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html

Feel free to contact us again at gen...@soe.ucsc.edu if you have any further questions.

---
Matthew Speir
UCSC Genome Bioinformatics Group

--