[maker-devel] representing gene tracks in gbrowse

[Barry Moore]

I'm not sure myself and I can't seem to find any of Carson's or Hadi's  
gbrowse conf files on our machines to see how they're doing this, but  
I'm forwarding this to Eric Ross as I think he may have dealt with  
this or a similar issue recently with SmedDB.  Eric, any ideas?

B

On Oct 13, 2009, at 1:08 PM, Mark Yandell wrote:

> 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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>
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