Re: [Gmod-ajax] Formatting using GFF notes and some other stuff

[Scott C. <sc...@sc...>]

Hi David,

That's correct; JBrowse, like Chado, uses interbase coordinates, so it
counts the spaces between bases rather than the bases themselves.
This makes all kinds of math easier, as well as make it easier to
unambiguously identify things like insertion and deletion points.

Scott


On Fri, Jul 30, 2010 at 9:22 AM, David Breimann
<dav...@gm...> wrote:
> 6. I noticed that when I click on the glyphs of feature parsed from GFF3
> files, the start coordinate shown on the pop-up window is shifted by -1
> relative to the actual coordinate written in the GFF file.
>
> On Tue, Jul 27, 2010 at 9:24 AM, David Breimann <dav...@gm...>
> wrote:
>>
>> Hi,
>>
>> 1. I would like to display some annotations from a GFF file on a single
>> track and control their color/glyph according to the content of the note in
>> the GFF (e.g. if 'Note=red' I would like this feature to be colored red, and
>> if 'Note=green' I would like it to be green).
>> 2. Can  I control for the height of the tracks (I know it can be done for
>> WIG tracks, but what about normal features tracks)?
>> 3. How can I control which tracks are shown by default?
>> 4. Suggestion: have a "reset view" in the browser (currently I have to
>> clear my browser history to return to the default view).
>> 5. Is there any ETA for the improvement of the WIG tracks (most
>> importantly adding a scale)?
>>
>> Keep up the good work,
>> Dave
>
>
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research