Greetings I am trying to create a GFF3-formatted file from knownGene, knownIsoforms and knownCanonical. (Most importantly, has anyone already done this?) I'm using the mySQL server directly, it's the easiest for me and should not be a burden to the server (but let me know). I see the join between knownGene and knownIsoforms on the name and transcript fields, but I'm looking for a gene name that is common to all the rows in knownIsoforms and I'm not finding it. For the cases I've examined, knownCanonical contains the same information as knownGenes. If I look in the browser at a member from clusterId=2, say uc001aac.2 I can see that it has the synonym FLJ0038 as do several others, but then all the other names are different. (These are pseudogenes and may therefore be a bad example.) Is there a field in a table somewhere that has the necessary one-to-many relationship between 'gene name' and clusterId? Am I misinterpreting knownIsoforms?
Thanks Mike Michael Muratet, Ph.D. Senior Scientist HudsonAlpha Institute for Biotechnology [email protected] (256) 327-0473 (p) (256) 327-0966 (f) Room 4005 601 Genome Way Huntsville, Alabama 35806 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
