Hi Alain, You could set up a filter using the related ensemblSource table, which shows coding/non-coding status. With the ensGene table selected in the Table Browser, hit the "filter: create" button and choose the ensemblSource table from the Linked Tables section. Create the filter such that "source doesn't match protein_coding".
To see the full list of possible values for the ensemblSource table, view its table schema in the Table Browser, and hit the "values" link in the info column for the source field. You should be aware that there are some other ways you could go about finding the non-coding transcripts: one way is to create a filter on ensGene where cdsStart=cdsEnd; another way is to filter out ensGene entries that do not have a protein listed in the protein field of the ensGtp table. Using the first method, I get a count of 43,096 genes that are annotated as something other than protein-coding. Using either of the other methods, I get a count of 88,332 genes that do not have an annotated coding region or associated protein. If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 2/17/12 2:27 PM, Alain Pacis wrote: > Hi, > > Is it possible to get a list of ncRNAs from the ensembl track? > I managed to do so with the refseq track by using NR_* in the name filter. > I am not quite sure how to employ the same filter for the ensembl track. > > Thank you. > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
