Hi Reece, To answer your first question, please see: https://lists.soe.ucsc.edu/pipermail/genome/2011-September/027099.html
The answers to questions #2 and #3 can be found on the RefSeq Genes track description page (see 'Methods' section): http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=refGene I hope this helps. Please contact us again at [email protected] if you have any further questions. Regards, --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 9/18/2011 2:27 PM, Reece Hart wrote: > Greetings- > > I have a few questions regarding RefSeq data in the public mysql hg19 > database. > > 1) Is there a way to know which version of a RefSeq appears in refFlat and > refAli (i.e., NM_000014.4 instead of NM_000014)? > > 2) What is the source of exon genomic coordinates? BLAT? > > 3) If the answer to (2) is BLAT, then are the NCBI coordinates available > also? What QC has been done to compare exon structures between BLAT and NCBI > (splign) coordinates? ( > > I've scoured the NAR 2011 paper, the table browser, the mailing list, > seqanswers, and google. Apologies if I somehow overlooked the answers to > these. > > Thanks, > Reece > _______________________________________________ > Genome maillist [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
