Hi Jennifer -- Thank you very much for your response and I apologize for my confusion. Just to confirm, the NCBI RefSeq RNA sequences are imported without alignment information to UCSC (and then aligned by BLAT), and as such to use the NCBI RefSeq exon definitions I need to obtain them directly from NCBI?
Thanks. -Dan On Wed, Sep 30, 2009 at 11:07 PM, Jennifer Jackson <[email protected]> wrote: > Hello, > The RefSeq sequences at UCSC are directly from the NCBI release. > Differences are likely due to the different programs used to generate the > alignment. To double check that the mRna is the same, extract the mRNa from > the Table browser or the track description page and compare it to the record > at NCBI. Also note that the update data is included on the track description > page, too. > We hope this helps, > Jennifer > > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "Daniel Herman" <[email protected]> wrote: > > > From: "Daniel Herman" <[email protected]> > > To: [email protected] > > Sent: Wednesday, September 30, 2009 4:25:45 PM GMT -08:00 US/Canada > Pacific > > Subject: [Genome] Refseq refGene version > > > > Hello -- > > > > I've been trying to make amino acid change predictions using UCSC > > genePred > > files (hg18; refseq refGene). However, it seems that for at least a > > couple > > transcripts (ex. NM_000256) the refGene exons are incorrect and > > different > > from NCBI Genbank, which I presume to be a version difference. > > > > I was considering rebuilding the refGene table (installing the UCSC > > source > > table for > > gtfToGenePred< > http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred>and > > trying to convert transcript definitions from NCBI or ENSEMBL), but I > > am > > wondering whether the refGene table will be updated in the near > > future. > > > > Thank you for any help. > > > > -Dan > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
