[Bioperl-l] gbrowse -- problem with gene model graph

Philip MacMenamin pm66 at nyu.edu
Thu May 13 14:51:17 EDT 2004


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)

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