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

[Lincoln Stein]

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>
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