Hi Stefanie, I double-checked your numbers for the hg19 database via the Table Browser, and I got all of the same counts.
For future reference, in case you want to do this yourself from the Table Browser, I used the "summary/statistics" button to show the various counts, and to find the number of protein-coding genes I added a filter on the knownGene table that used the free-form query cdsStart!=cdsEnd. Also, in case querying the MySQL database directly would be easier for you, instructions for accessing it are here: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 -- Brooke Rhead UCSC Genome Bioinformatics Group Stefanie Gerstberger wrote on 9/27/10 5:36 PM: > Hi, > I would like to cite the current list of genes contained in the UCSC genome > browser known as the "UCSC genes". From the downloads from your website I > noticed that I got a different number of canonical proteins when I uploaded a > file (by 3000 protein coding genes higher) than if I used the knowncanonical > list and parsed through it myself. I checked for the Pumilio proteins and > found > in one case that 2 pumilio isoforms were listed from the directly downloaded > canonical gene file even though this accession number was not listed in the > knowncanonical it was nevertheless found in the fasta file. > I got following count of genes: > > total UCSC genes (containing all isoforms) : 77614 > number of "canonical" UCSC genes (one isoform per gene locus): 27297 > total protein coding UCSC genes (containing all isoforms): 62378 > number of "canonical" UCSC protein coding genes (one isoform per gene locus): > 21018 > > (the number of protein coding genes was generated by parsing myself through > the > files). > Please could you let me know whether these numbers are currently correct, > > Thank you very much, > > > Stefanie > > > --------------------------------------------------- > Stefanie Gerstberger > graduate student in Chemical Biology > Tri-Institutional Program > Cornell University, > Rockefeller University, > Memorial Sloan Kettering Cancer Center > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
