Hello, I am looking to extract coding sequence for exons. Most genes tables, like refGene on hg18/hg19, include a field called "exonFrames", which contains values 0,1,2 and can be used to translate each exon start-stop genomic text according to the right frame. So far so good. However, certain genes tracks, including knownGene for all species, or even refGene for rn4, do not contain that field. Moreover, because certain genes do not start with a start codon (or, in other words, have an "incomplete start"), one cannot just assume that cdsStart is aligned to a frame and start translating all exons according to that. So, how does UCSC display the codon information when zooming in to a knownGene (or a refGene in rn4)? Which table is that information stored? Where is the missing exonFrames info?
Thanks in advance, Y. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
