[maker-devel] Maker consensus

[Carson Holt]

I'm sorry I don¹t' understand question 1.  You are you missing resulting
fasta files, correct?  Did your resulting GFF3 file have any features of
type "gene"?  Did you run fasta_merge after running gff3_merge?

Could you give me more details on what you are trying to do, so I can take a
stab at question 2 as well.

Thanks,
Carson



From:  Diana LeDuc <diana_leduc at eva.mpg.de>
Reply-To:  Diana LeDuc <diana_leduc at eva.mpg.de>
Date:  Friday, 10 May, 2013 10:44 AM
To:  <maker-devel at yandell-lab.org>
Cc:  Gabriel Renaud <gabriel_renaud at eva.mpg.de>, Janet Kelso
<kelso at eva.mpg.de>, Torsten Schoeneberg
<torsten.schoeneberg at medizin.uni-leipzig.de>
Subject:  [maker-devel] Maker consensus

  
   
  

Dear maker developers,
  

I am a phD student working on de novo assembly and annotation of a bird
genome. I used Maker as annotation pipeline, which ran very well, and I
obtained different annotations with evidence from Augustus gene predictor,
small EST dataset from my organism and protein sequences from chicken,
turkey and zebrafinch. I could combine the different gff files from
different scaffolds into one gff file with annotations for the entire
genome.
  

I now have two questions:
  

1. What could be the reason that I haven't gotten the protein.fasta and
trancript.fasta files
  

2. How can I obtain a consensus gene list of different evidences from maker?
What I would actually need is the scaffold, coordinates and annotation (gene
name) according to the 3 other bird species.
 Thank you in advance.
  
   
  
 Best regards, 
  
   
  
 Diana Le Duc 
  
   
  
 --  
 
Max Planck Institute for Evolutionary Anthropology
Department of Evolutionary Genetics
Deutscher Platz 6 
D-04103 Leipzig 
 
Phone +49 (0)341-3550-554
 www.eva.mpg.de <http://www.eva.mpg.de>
 
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