[Genome] question: non-protein coding genes

[Brooke Rhead]

Hello Elana,

To get all of the non-protein-coding UCSC Genes in BED format, go to the 
Table Browser (the "Tables" link at the top of the page) and select the 
clade, genome and assembly of interest.  Then select:

group: Genes and Gene Prediction Tracks
track: UCSC Genes
table: knownGene
region: genome
output format: BED - Browser Extensible Data
output file: enter a filename to save the results to your computer

Then hit the "filter: create" button, and in the free-form query box 
enter: cdsStart=cdsEnd and hit submit.  Now hit "get output".

Note that only the "UCSC Genes" tracks in hg18 and mm9 contain 
non-protein-coding genes (the older "Known Genes" tracks do not).

If you have further questions, please feel free to write back to this 
mailing list address.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Miriami Elana wrote:
> Hello,
> 
> I am interested in non-protein coding genes from all Known Genes (the
> coordinates
> in a bed file with the name of the gene). How can I get it using the UCSC genome
> browser?
> 
> Thank you very much,
> 
> Miriami Elana
> Yale University
> Department of Biology and MCB
> 219 Prospect St
> New Haven, CT 06511
> USA
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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