Hello Greetz, Which assemblies do you need to get RefSeq gene symbols for? The refGene tables in most of our assemblies have a "name2" field that already contains the gene symbol.
The answer to your first question about identical RefSeq IDs with different chromosome positions is that the RefSeq track is created by aligning RNAs to the genome; multiple alignments are not entirely uncommon: Methods RefSeq RNAs were aligned against the mouse genome using blat; those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept. (from http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=refGene) If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 5/25/12 5:28 AM, [email protected] wrote: > > > Hey, > > I need to assign RefSeq transcripts to their respective genes and did > this by joining the primary table refGene to refFlat. I encountered > two problems here: > > a) There seem to be RefSeq transcripts with identical RefSeq ids, but > differing chromosome positions (for mm9 e.g. NM_011253). How can that > be? > > b) In the secondary table (refFlat) the RefSeqID as a foreign key is > not unique either, so I get duplicate results in the final view (that > is duplicates for each single occurrence of the id in the primary > table) > > > Is there a better table from which to retrieve the gene names for the > refGene transcripts (in which the RefSeqID is unique)? > > I tried the table kgXref as well but in that one there doesn't even > seem to be a gene symbol for every RefSeqID. > > > > Greetz _______________________________________________ Genome > maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
