Excellent, thanks for this Jennifer! On Tue, Apr 13, 2010 at 10:35 PM, Jennifer Jackson <[email protected]> wrote:
> Small addition: > > If using this method to extract mRNA sequences, be sure to exclude rows > from kgXref that also do not have a mRNA identifier. There are only 5 of > these in hg19: > > mysql> select kgID, geneSymbol, description from kgXref where mRNA like ""; > +------------+------------+----------------- > | kgID | geneSymbol |description > +------------+------------+----------------- > | uc010tyt.1 | abParts | Parts of antibodies, mostly variable regions. | > | uc002stl.2 | abParts | Parts of antibodies, mostly variable regions. | > | uc010fhm.2 | abParts | Parts of antibodies, mostly variable regions. | > | uc010ytr.1 | abParts | Parts of antibodies, mostly variable regions. | > | uc011aim.1 | abParts | Parts of antibodies, mostly variable regions. | > +------------+------------+----------------- > 5 rows in set (0.00 sec) > > > > On 4/13/10 2:23 PM, Jennifer Jackson wrote: > >> Hello again, >> >> Yes, that would be a correct way to interpret the table contents. >> >> Thanks! >> Jen >> >> --------------------------------- >> Jennifer Jackson >> UCSC Genome Informatics Group >> http://genome.ucsc.edu/ >> >> On 4/13/10 12:20 PM, Bio X2Y wrote: >> >>> Hi, >>> >>> >>> Concerning the Known Genes annotation, is it correct to say that any >>> transcript whose kgxref row contains empty values for spID, spDisplayID, >>> refseq and protAcc is a GenBank mRNA based transcript? >>> >>> >>> Thanks for your help! >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
