[maker-devel] representing gene tracks in gbrowse

[Eric Ross]

I don't run gbrowse against a chado database, i just use a seqfeature  
database, but if you haven't tried "processed_transcript" as your  
glyph type that is what works best for my implementation.

For Scott here's a bit of the GFF3 from Maker output:

v31.023451      maker   gene    9114    9474    .        
+       .       ID=maker-v31.023451-augustus-gene-0.2;Name=maker- 
v31.023451-augustus-gene-0.2;
v31.023451      maker   mRNA    9114    9474    .        
+       .       ID=maker-v31.023451-augustus-gene-0.2- 
mRNA-1;Parent=maker-v31.023451-augustus-gene-0.2;Name=maker-v31.023451- 
augustus-gene-0.2-mRNA-1;_AED=0.24;_QI=2|0|0|0.5|0|0|2|1|104;
v31.023451      maker   exon    9114    9328    0.71     
+       .       ID=maker-v31.023451-augustus-gene-0.2-mRNA-1:exon: 
9583;Parent=maker-v31.023451-augustus-gene-0.2-mRNA-1;
v31.023451      maker   exon    9375    9474    0.71     
+       .       ID=maker-v31.023451-augustus-gene-0.2-mRNA-1:exon: 
9584;Parent=maker-v31.023451-augustus-gene-0.2-mRNA-1;
v31.023451      maker   CDS     9116    9328    .       +        
0       ID=maker-v31.023451-augustus-gene-0.2-mRNA-1:cds: 
9292;Parent=maker-v31.023451-augustus-gene-0.2-mRNA-1;
v31.023451      maker   CDS     9375    9473    .       +        
0       ID=maker-v31.023451-augustus-gene-0.2-mRNA-1:cds: 
9293;Parent=maker-v31.023451augustus-gene-0.2-mRNA-1;


Eric

On Oct 13, 2009, at 1:20 PM, Barry Moore wrote:

> 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.
>>>
>>> This email and any attachments thereto may contain private,
>>> confidential, and privileged material for the sole use of the
>>> intended recipient.  Any review, copying, or distribution of this
>>> email (or any attachments thereto) by others is strictly
>>> prohibited.  If you are not the intended recipient, please contact
>>> the sender immediately and permanently delete the original and any
>>> copies of this email and any attachments thereto.
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at yandell-lab.org
>>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>>
>> -----------------------------------------------------------------------
>> Scott Cain, Ph. D. scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at yandell-lab.org
>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at yandell-lab.org
>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>