Re: Scroll buttons, negative coordinates, key positions
Oh, what you have now is a mixture of GFF2 and GFF3. To make it all
consistent, you want to change the chromosome lines to GFF2, like this:
2 assembly chromosome 1 234607100 . . . Sequence 2
Where there are 9 tab delimited columns (no tab between the "Sequence"
and the "2").
Scott
On Mon, 2008-05-05 at 14:09 -0500, Taner Z. Sen wrote:
> Hi Scott,
>
> The line was slightly different, but according to your suggestion, I
> changed it to:
> 2 assembly chromosome 1 234607100 . . . Sequence ID=2;Name=2
>
> (deleting "Sequence" doesn't change results)
>
> But the result is the same.
>
> The full gff files is here:
> http://grinch8-2.gdcb.iastate.edu/maize_copy.gff
>
> Any other suggestions?
>
> At 10:35 AM 5/5/2008, Scott Cain wrote:
> > Hi Taner,
> >
> > The problem you are seeing is almost certainly a result of your
> > reference sequence not being correct. The overview panel should
> > show
> > the entire length of chromosome 2 with a red box around the region
> > you
> > are looking at in the details panel. When you see what you are
> > seeing
> > (an overview that starts and stops where your detail view starts and
> > stops), it is usually because you don't have a valid reference
> > sequence
> > line. Do you have something that defines what '2' is, like this:
> >
> > 2 . chromsome 1 10000000 . . . ID=2;Name=2
> >
> > Scott
> >
> > On Mon, 2008-05-05 at 09:35 -0500, Taner Z. Sen wrote:
> > > I installed GBrowse and uploaded some maize data.
> > > http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
> > >
> > > I have a few problems with the data display:
> > >
> > > 1) The scroll buttons don't work:
> > > a) go to
> > http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
> > > b) click example "2:2,000,000..4,000,000"
> > > c) Click left or right arrows of the "scroll". They don't work.
> > >
> > > 2) Negative coordinates appear:
> > > a) go to
> > http://grinch8-2.gdcb.iastate.edu/cgi-bin/gbrowse/maize/
> > > b) click example " BAC:AC177838"
> > > c) Choose "show 500kbp"
> > >
> > > There are negative coordinates on the left hand side.
> > >
> > >
> > > 3) I want key positions to appear on the left when the page first
> > > loads. It seems that there are only two options for "keystyle":
> > > beneath and between to put in the conf file. Is there any other
> > way
> > > except choosing the corresponding radio button in the "display
> > > settings" after the page loads? (keystyle=left didn't work)
> > >
> > > Do you have any suggestion to fix these issues?
> > >
> > >
> > > Thank you very much,
> > > Taner
> > > taner@...
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
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> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.
> > cain@...
> > GMOD Coordinator (http://www.gmod.org/ )
> > 216-392-3087
> > Cold Spring Harbor Laboratory
>
> Taner Z. Sen, Ph.D.
> Computational Biologist, USDA-Agricultural Research Service
> Collaborator Assistant Professor, Dept. of Genetics, Development and
> Cell Biology
> Bioinformatics and Computational Biology Program
> Iowa State University
> 1025 Crop Genome Informatics Lab
> Ames, IA 50011
> Phone: (515) 294-5326
> Fax: (515) 294-8280
> taner <at> iastate. edu
> http://www.public.iastate.edu/~taner/
>
> -------------------------------------------------------------------------
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--
--
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl@...
GMOD Coordinator (http://www.gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory
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