[Gmod-gbrowse] [Gmod-help] Re: can't view detailed view

[Josh Goodman]

I ran the X through the GFF validator and found a few minor problems that 
may or may not be contributing to this.  The problems include features 
that use the Name tag twice in a single line and a capitalized field tag 
that is not an official attribute column tag ('PCR_template').  Both of 
these problems are not specific to the X so it may not be related to your 
problem.  I'll make sure that they are corrected for our next release.

Other than this there were no obvious issues, although the validator tends 
to spit out a large number of false positives which makes it easier to 
miss the real errors.

Cheers,
Josh

On Fri, 1 May 2009, Lincoln Stein wrote:

> I'm sorry you're having this problem. If I understand correctly, the problem
> occurred only after you loaded the X chromosome, and now affects all
> chromosomes except for YHet?
> 
> Could you try clearing out the database and loading chromosomes in the order
> 2L, 2R, 3L, 3R, 4, X and check whether the problem appears after each
> chromosome is loaded? I am hoping that this is an isolated problem in the
> chromosome X GFF3 file; this will help narrow it down.
> 
> Lincoln
> 
> 2009/4/30 Miquel Ràmia <miquel.ramia at uab.cat>
> 
> > I downloaded the files from
> > ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff/
> > (r5.16 was the current few weeks ago)
> >
> > Here are 2 screenshots, searching both by crhomosome name, the YHet
> > looks good, and the X shows the "match" screen, any click in the results
> > (only one in this case) always returns the "match" screen
> >
> >
> >
> >
> > El dc 29 de 04 del 2009 a les 11:46 -0700, en/na Dave Clements, GMOD
> > Help Desk va escriure:
> > > Hi Miquel,
> > >
> > > Can you send screenshots of what it looks like when it working and
> > > when it isn't?
> > >
> > > Also are the GFF files from
> > > ftp://ftp.flybase.net/releases/FB2009_04/dmel_r5.17/gff/ ?
> > >
> > > I don't have any explanation for this behavior, yet.
> > >
> > > Thanks,
> > >
> > > Dave C.
> > >
> > > Was this helpful?  Let us know at
> > http://gmod.org/wiki/Help_Desk_Feedback
> > >
> > > Learn more about GMOD at SMBE & Arthropod Genomics:
> > >  http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
> > >  http://www.k-state.edu/agc/symp2009/seminar.html
> > >
> > >
> > > 2009/4/27 Miquel Ràmia <miquel.ramia at uab.cat>
> > > >
> > > > Hi,
> > > >
> > > > I'm running Gbrowse 1.69 in a Linux CentOS. I'm trying to upload the
> > > > D.melanogaster GFF data from flybase to a mysql database. And I have a
> > > > problem: In some chromosomes , via searching landmark/region by name, I
> > > > can view de detailed view and tracks, or an overview with the "more
> > than
> > > > 1.3 Mb not displayed" message; I zoom in and no problem.
> > > >
> > > > But with other chromosomes I can only see a "match" r with no zoom
> > > > option and without detailed view or anything.
> > > >
> > > > I tried loading de GFFs chromsome by chromosome (in this order : YHet,
> > > > U, X, 4, 3R ...). At first I could view the YHet and U details and
> > > > tracks with no problem, but after loading X data I couldn't view U
> > > > details but the YHet only. The same with all the chromosomes loaded
> > into
> > > > the database.
> > > >
> > > > Any idea ?
> > > >
> > > > Thank you!
> > > >
> > > > Miquel Ràmia
> > > >
> > > >
> > > >
> > > >
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> 
> 
> 
> -- 
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
>