When I was using the knownCanonical table to find the canonical transcript for MYC, I find that there are two entries. See below. I also included some fields from hg19.kgXref fields. Is there an accepted method to determine which one is the most "canonical" transcript? Perhaps use the transcript where there is a "NM" as the prefix in refseq?
Thanks, Andrew #hg19.knownCanonical.chrom hg19.knownCanonical.chromStart hg19.knownCanonical.chromEnd hg19.knownCanonical.clusterId hg19.knownCanonical.transcript hg19.knownCanonical.protein hg19.kgXref.kgID hg19.kgXref.mRNA hg19.kgXref.spID hg19.kgXref.spDisplayID hg19.kgXref.geneSymbol hg19.kgXref.refseq chr8 128748314 128753678 24861 uc003ysi.2 uc003ysi.2 uc003ysi.2 NM_002467 A0N2G3 A0N2G3_HUMAN MYC NM_002467 chr8 128806778 129113498 24862 uc010mdq.2 uc010mdq.2 uc010mdq.2 NR_003367 MYC NR_003367 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
