[Gmod-help] GFF3 uploads

[Scott Cain]

Hi Rohan,

I don't think it will be possible to do what you want with uploaded GFF files.

While it is trivial to color things differently in GBrowse from a
configuration file, it is not possible from an uploaded file because
it requires the use of perl callbacks, which are generally not allowed
in uploaded files because of security implications.

For the other question, I think what you mean is that you want things
to line up horizontally as you move along the chromosome, instead of
everything moving to the top of the track when there is nothing else
above it.  Is that right?  If so, that can't be done either: there is
no way of preventing features from moving to the top of the track.  If
that's not what you meant, there is a "sort_order" option that can be
included in a uploaded configuration, with options "left" (the left
coordinate), "right", "low score", "high score" or "name".

Scott


On Sun, Jun 27, 2010 at 8:20 PM, Rohan Bansal <bansal at princeton.edu> wrote:
> To The Help Desk,
>
>
> I am a user that creates simple gff3 files and uploads them to plasmodb.org,
> which hosts an instance of gbrowse online.
>
> Is it possible to make a specific feature have different colors for
> different objects?
>
> i.e., If I'm making a feature with many different objects in it, could I
> specify, within each line (object), what color I wanted the object to be?
>  Or possibly group specific objects together by color?
>
> If not that, then is it possible that I can group several features so that
> they will appear on the same line?  I have am lining up motifs and I want to
> be able to distinguish between them by color coding, but if I have them on
> several lines, the data becomes too spread out.
>
>
> I would like to restate that this is for uploaded gff3 files.
>
>
> Thank you,
>
> Rohan Bansal
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research