Hi Dan, Yes, this is exactly correct for RefSeqs and many other tracks (in particular data from NCBI). You might want to create a custom track of the NCBI alignments and compare directly in the context of UCSC Genes and other sources. Good luck, Jennifer
------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Daniel Herman" <[email protected]> wrote: > From: "Daniel Herman" <[email protected]> > To: "Jennifer Jackson" <[email protected]> > Cc: [email protected] > Sent: Wednesday, September 30, 2009 8:39:34 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] Refseq refGene version > > 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
