[maker-devel] Maker consensus

[Diana LeDuc]

Hi Carson,

Thank you for the quick answer.
I ran gff3_merge to merge all the gff files and this resulted in a gff file,
which has these type of fields:
scaffold32239   blastx  protein_match   22905   34500   174     +       .
      ID=scaffold32239:hit:976144;Name=ENSTGUG00000000198|ENSTGUT00000000219|DSCAML1-2039;
scaffold32239   blastx  match_part      22905   23045   174     +       .
      ID=scaffold32239:hsp:2806529;Parent=scaffold32239:hit:976144;Name=ENSTGUG00000000198|ENSTGUT00000000219|DSCAML1-2039;Target=ENSTGUG00000000198|ENSTGUT00000000219|DSCAML1-2039
172 218;Gap=M47;
In comparison to the dpp_contig test file, I am missing est2genome evidence,
most probably because my est data set is pretty poor. I have blastx and
protein2genome evidence though.

My goal is to extract the genes that could be annotated on the scaffolds. In the
gff files the hits overlap most of the times, I can visualize this properly in
apollo: for example one scaffold hits DSCAML gene in both zebrafinch and
chicken, but extracting the coordinates between which this scaffold fits this
annotated gene is difficult from the gff. Manually curating the genes is also
not an option, since I am trying to do this for a 1.7Gb genome.

I hope this explains better what we are after.

Thank you once again.

Best regards,

Diana
On May 10, 2013 at 6:13 PM Carson Holt <carsonhh at gmail.com> wrote:

>  I'm sorry I don’t' 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 <mailto:diana_leduc at eva.mpg.de> >
>  Reply-To: Diana LeDuc < diana_leduc at eva.mpg.de
> <mailto:diana_leduc at eva.mpg.de> >
>  Date: Friday, 10 May, 2013 10:44 AM
>  To: < maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org> >
>  Cc: Gabriel Renaud < gabriel_renaud at eva.mpg.de
> <mailto:gabriel_renaud at eva.mpg.de> >, Janet Kelso < kelso at eva.mpg.de
> <mailto:kelso at eva.mpg.de> >, Torsten Schoeneberg <
> torsten.schoeneberg at medizin.uni-leipzig.de
> <mailto: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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