[maker-devel] representing gene tracks in gbrowse

[Mark Yandell]

Thanks Scott. 

Don't know if Carson is on line today or not, but maybe Barry or Hadi could send something. Guys?
--mark


Mark Yandell
Associate Professor of Human Genetics
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707
________________________________________
From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] On Behalf Of Scott Cain [scott at scottcain.net]
Sent: Tuesday, October 13, 2009 12:34 PM
To: Shane Brubaker
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] representing gene tracks in gbrowse

Hi Shane,

I realize the MAKER folks probably already know what it looks like,
but can you send a snippet of the GFF3 that gets loaded into Chado so
I can take a look?  Configuring it blind is tough :-)

Thanks,
Scott

On Oct 13, 2009, at 2:26 PM, Shane Brubaker wrote:

> Hi, can someone recommend for me the proper way to configure a
> gbrowse track for the display of maker genes?
>
> I am running maker and producing gene models from augustus and
> snap.  I then load the data into chado.  This produces a feature for
> an mRNA with a polypeptide, and exons.
>
> No matter what I do to change the track configuration, I see a solid
> block instead of seeing the exons represented explicitly as in a
> typical gene model.  However my "protein_matches" track does appear
> segemented when I change the glyph to segments.
>
> In fact it is a bit strange, when I change the color or height I
> don't really see any change ... but if I change the key for example
> I will see the change when I refresh.
>
> Can anyone tell me the proper way to configure the track?
>
> Here is my current configuration:
>
> [Genes]
> feature = gene
> glyph = transcript
> base = 1
> ignore_sub_part = CDS intron
> fgcolor = blue
> height = 15
> linewidth = 2
> key = Named gene
>
>
>
> Thanks for your help.
>
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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





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