RE: [GMOD-devel] GBrowse search question, display problem

[Scott C. <ca...@cs...>]

Nothing jumps out at me from the config file, so I wonder if it could be
a database problem.  One easy way to get the required information is to
turn on query logging, reload a known-broken image, get the queries and
run them in mysql's command line.  Look for anomalies--figure out if
those features are being retrieved and if not, why not.  If they are
being retrieved and not drawn, then it is a software error that we will
have to track down.  In particular, I am curious what the value of fbin
is for the missing features.  Perhaps you could send me the result of 

  select * from fdata where fref='Chr1' and ftypeid = ##

where ## is the ftypeid of RGD_QTL.

Thanks,
Scott


 

On Mon, 2003-10-13 at 13:04, Nie, Jeff wrote:
> Hi, Scott
> Here is the config file we used to. 
> Jeff
> 
> -----Original Message-----
> From: Scott Cain [mailto:ca...@cs...] 
> Sent: Monday, October 13, 2003 11:35 AM
> To: Simon Twigger
> Cc: gmod list; jn...@mc...
> Subject: Re: [GMOD-devel] GBrowse search question, display problem
> 
> Simon,
> 
> It is very strange that it your features show up in the overview and not
> in the detail view.  At first I thought it might be a query problem
> (overlaps versus contains or something like that), but A) gbrowse always
> does a overlaps query here, and 2) if I expand the view, there are
> features that should be entirely contained in the detail view and still
> are not there, like:
> 
> http://www.hpc.mcw.edu/mod_perl/gbrowse?name=Chr1%3A75481992..122169351;sour
> ce=rgd_903;width=800;label=RGD_QTL-RGD_curated_genes
> 
> where Map1 should be there but is not.
> 
> The other available options are config problems and data problems.  Can
> you send the conf file so I can take a look?
> 
> Thanks,
> Scott
> 
> On Mon, 2003-10-13 at 12:19, Simon Twigger wrote:
> > Hi there,
> > 
> > Quick GBrowse question and potential bug report.
> > 
> > Can you join search terms when you search for a feature, eg. 'Bp* or  
> > Slc*' to bring up in our case everything starting with Bp (such as  
> > Blood pressure QTLs) and everything starting with Slc (solute  
> > transporter genes). Currently running either of these queries alone  
> > brings back a great map of the genome with the QTLs or the genes listed  
> > with their locations shown in the overview plot for each chromosome. If  
> > we could combine the searches then the plots that came back would be  
> > even more useful - Locations of Solute transporter genes and the Blood  
> > pressure QTLs on one image.
> > 
> > I dont know how painful such a boolean feature would be to add but it  
> > would make the searching/browsing feature of GBrowse very powerful I  
> > think.
> > 
> > Potential Bug report:
> > If I have a feature (eg QTL) that is larger than the window being  
> > displayed, the QTL doesnt appear on the main track.
> > 
> > Eg. try this link:
> > 
> > http://www.hpc.mcw.edu/mod_perl/
> > gbrowse?name=Chr1%3A63810346..93810346;source=rgd_903;width=800;label=RG 
> > D_QTL-RGD_curated_genes
> > 
> > This should show 3 QTL in this region (see the overview plot: Rtc1,  
> > Scl6 and Bp96), however, only Scl6 is shown as it is entirely within  
> > the region being displayed, Rt1 and Bp96 are not shown. This doesn't  
> > tend to happen with other features, so perhaps we should look at what  
> > glyphs we are using... Any thoughts?
> > 
> > Cheers,
> > 
> > 	Simon.
> > 
> > 
> > ------------------------------------------------------------------------ 
> > --------------------------
> > Simon Twigger, Ph.D.
> > Assistant Professor, Bioinformatics Research Center
> > 
> > Medical College of Wisconsin
> > 8701 Watertown Plank Road,
> > Milwaukee, WI, 53226
> > tel. 414-456-8802, fax 414-456-6595
> > 
> > 
> > 
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory