[Bioperl-l] gbrowse -- problem with gene model graph
pm66 at nyu.edu
Fri May 14 11:59:15 EDT 2004
(I sent this yesterday, but I think it got lost... appologies if it
I am assuming that I am missing something here...
I have downloaded GBrowse-1.61, pointed it to 02.wormbase.conf release_1_61,
which points to a local mySQL db, running WS123. This DB was created using
bulk_load_gff.pl with the WS123 GFF file massaged by process_wormbase.pl.
Everything almost works perfectly... except that the gene models have no
introns, and the frame usage for the CDSs are not correct. On a DB with new
model GFF stuff loaded that was not massaged by the process_wormbase script
there no introns. (Same issue with the CDS frame usage.) The same thing
happens when you point it at WS120 etc. So, as I said, I must be missing
something. If I point back to an old wormbase GFF SQL DB, there are no
problems like this.
(Aside: I noticed the same sort of thing happening when the model changes
occured, and the issue was essentially sorted out by using the
processed_transript like aggregator)
More information about the Bioperl-l