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

Lincoln Stein lstein at cshl.edu
Mon May 24 12:57:32 EDT 2004

It might be a better idea to use the configuration file located in the 
wormbase releases rather than in the gbrowse release.  The former is 
guaranteed to be up to date with wormbase model changes.

To make it easier for you, I'll put the current configuration file 
into the wormbase download directory parallel with the gff data 



On Friday 14 May 2004 11:59 am, Philip MacMenamin wrote:
> (I sent this yesterday, but I think it got lost... appologies if it
> arrives twice)
> Hi,
> 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.
> (http://search.cpan.org/~birney/bioperl-1.4/bioscripts.pod#scripts/
> 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)

Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

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