[maker-devel] representing gene tracks in gbrowse

[Scott Cain]

Hi Shane,

Please keep your responses on the list, so everyone can see the  
discussion.

First, I missed the part about it not changing (which, I realize, was  
a pretty important part of the email).  You need to make sure that you  
set "cache time    = 0" in your configuration file, or GBrowse will  
used a cached image, not realizing you changed the conf file.  It  
doesn't use the cached image when you change the track key, because  
that is part of how it looks up the image.

For the data you sent me, you should be able to use the gene glyph,  
which is a little better than related transcript glyphs, since it  
knows how to deal with splice variants.

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