Hi Brooke, Thanks for your reply - its helpful!
Just to be sure, may I ask what usually follows when theres a change of id? Is it just an id change per se or any modification of bases/coordinates etc? Thanks again! On 08-Oct-2011, at 2:46 AM, Brooke Rhead wrote: > Hi, > > The issue is that the RefSeq identifier in your example has been > replaced by RefSeq. If you go to: > > http://www.ncbi.nlm.nih.gov/nuccore/NM_214677.1?report=genbank > > You will see the message: > > NCBI Reference Sequence: NM_214677.1 > This sequence has been replaced by NR_026707. > > The reason you can still find a reference to it in the knownGene track > on hg18 is that that track was updated in 2009 (see the "Data last > updated" note at the top of the page). On the other hand, the refGene > track is updated on our site every day, so this is normal. > > Admittedly, our error message is not very informative. I have submitted > a request to our engineers to change it so that it is more obvious what > the problem is. > > I suggest looking for the rest of your missing NMs in NCBI's Nucleotide > database (http://www.ncbi.nlm.nih.gov/nuccore/) to see if they have > changed or have been replaced. You should be able to find the current > set of RefSeq identifiers in the Genome Browser. > > If you have further questions, please contact us again at > [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 10/7/11 2:35 AM, Luqman Hakim Bin Abdul Hadi wrote: >> Hi UCSC team, >> >> I'm noticing an inconsistency of a large scale between the Browser >> andthe Table. >> In particular, I have a list of NMs (refseq ids) which I need to get > its coordinates using 'track: RefSeq Genes' and 'table: refGene'. For > brevity, lets use NM_214677 (there are other genes in my list with the > same problem) >> >> An error inn the Table browser led me to suspect that NM_214677 >> could be missing: >> "Note: 1 of the 1 given identifiers (e.g. NM_214677) have no match >> intable refGene, field name or in alias table refLink, field name. Try the > "describe table schema" button for more information about the table and > field." >> >> I proceeded to try almost every possible table but I could not find > NM_214677. I was beginning to resign to my fate until I checked the > Genome Browser and found NM_214677 here: > http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc002mie.1&hgg_prot=Q9H2X3-2&hgg_chrom=chr19&hgg_start=7734080&hgg_end=7740491&hgg_type=knownGene&db=hg18&hgsid=216140513 >> >> However, the link in the page (under 'Other Names for This Gene'), > which I suppose should link me to another page gave me this error: >> "Couldn't find NM_214677 in refLink table - database inconsistency." >> >> I hope a fix is already in place, otherwise is this 'normal'? Is >> there any other particular way that I can search for my missing NMs? >> >> Thanks! >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
