[maker-devel] Maker: accessory scripts

[Carson Holt]

You seem to be running this in a very odd way.  First the GFF3 is not
correctly formatted. There are lines containing score=1 (all by itself)?  I
believe this may be coming through because you are trying to pass in
augustus predictions as GFF3 and that input is malformed.  All of your
Augustus models are also single exon genes, but they are very long and do
not even correspond to proper ORFs.  The EST evidence is spliced and is thus
contradicting the augustus model (they don't support each other).  If you
want MAKER to be able to use the evidence as feedback for the model, you
need to let MAKER run augustus.  Otherwise it is only able to accept or
reject the model from the GFF3 (nothing more ­ no attempt at consensus).

Perhaps if you supply you input dataset and control files we can help you
get the best settings.  You would need to provide the Augustus species set
you are using as well (contained in a directory in
Š/augustus/config/species).

--Carson


From:  Innocent Onsongo <onson001 at umn.edu>
Date:  Friday, 7 June, 2013 2:08 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Carson Holt <carson.holt at oicr.on.ca>, "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>, Barry Moore <barry.utah at gmail.com>
Subject:  Re: [maker-devel] Maker: accessory scripts

Carson, 

I have attached the full gff3 for the contig together with a screen shot
from IGV with regions I was expecting Maker to make a consensus call. The
region on question is CGS00003:5264784-5273457. I will greatly appreciate
any insights. 



Thanks, 

Getiria 




On Thu, Jun 6, 2013 at 8:55 AM, Carson Holt <carsonhh at gmail.com> wrote:
> One thing to keep in mind is the strandedness of the evidence and the model
> (they must be on the same strand).  Further protein evidence is only valid
> support if it is in the same reading frame as the model.
> 
> Could you send the full GFF3 for the contig (I need features and GFF3 internal
> fasta) and the coordinates of the region in question, and I can take a look?
> Also if you can, it would be good to let maker run Augustus as well with the
> species file rather than just passing in the GFF3.  This is because MAKER can
> only talk to Augustus to generate competing hint based models if you provide
> the species.
> 
> Thanks,
> Carson
> 
> 
> From:  Innocent Onsongo <onson001 at umn.edu>
> Date:  Wednesday, 5 June, 2013 1:10 PM
> To:  Carson Holt <carsonhh at gmail.com>
> Cc:  Carson Holt <carson.holt at oicr.on.ca>, "maker-devel at yandell-lab.org"
> <maker-devel at yandell-lab.org>, Barry Moore <barry.utah at gmail.com>
> 
> Subject:  Re: [maker-devel] Maker: accessory scripts
> 
> I checked visually in IGV and there are some exons in the predicted model with
> protein and EST support but the maker output GFF only has match_part and
> protein_match in column 3. Does that mean Maker doesn't deem any of the
> evidence sufficient to make a gene model prediction?
> 
> I guess I am somewhat surprised I am not getting any exons predicted by Maker.
> Is there a parameter I can alter to reduce the threshold at which Maker makes
> this call? I have attached the first 400 lines of one of my GFF files together
> with the control file (maker_opts.ctl) just in case they might be useful.
> 
> Getiria 
> 
> 
> On Wed, Jun 5, 2013 at 9:47 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> Also, just a note, models are rejected if they have no protein or EST
>> support.  This is because ab inito predictors over predict (you may have 10
>> false positives for every true positive in some genomes for example).
>> 
>> --Carson
>> 
>> 
>> 
>> From:  Carson Holt <carsonhh at gmail.com>
>> Date:  Wednesday, 5 June, 2013 10:44 AM
>> To:  Innocent Onsongo <onson001 at umn.edu>, Carson Holt
>> <carson.holt at oicr.on.ca>
>> 
>> Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>, Barry Moore
>> <barry.utah at gmail.com>
>> Subject:  Re: [maker-devel]  Maker: accessory scripts
>> 
>> All maker gene annotations will be of the format  gene/mRNA/exon/CDS.
>> Anything in the format match/match_part is an evidence alignment or rejected
>> model and is there for reference purposes.  If you want to upgrade all of the
>> rejected loci to gene annotations, set keep_preds=1 in the control files.  If
>> you want to upgrade a subset of rejected models to a full annotation, create
>> a list of IDs (one per line) then give them to the attached script.
>> gff3_preds2models was previously deprecated and no longer part of the maker
>> distribution, but the attached script is an updated version with the same
>> functionality. 
>> 
>> --Carson
>> 
>> 
>> 
>> From:  Innocent Onsongo <onson001 at umn.edu>
>> Date:  Wednesday, 5 June, 2013 12:35 PM
>> To:  Carson Holt <carson.holt at oicr.on.ca>
>> Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>, Barry Moore
>> <barry.utah at gmail.com>
>> Subject:  [maker-devel]  Maker: accessory scripts
>> 
>> I was able to successfully ran Maker and now want to converts the gene
>> prediction match/match_part format to annotation gene/mRNA/exon/CDS format. I
>> looked at the tutorial and the script gff3_preds2models
>> is supposed to do this conversion. How do I access this script. It is not in
>> /maker/2.28-beta/bin/
>> 
>> Also, in running gff3_preds2models <gff3 file> <pred list>  is <pred list>
>> the file I used for pred_gff=?
>> 
>> Long story short, how do I transform the GFF output from Maker to the more
>> traditional annotation of exon/intron?
>> 
>> Thanks,  
>> Getiria
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma
>> ker-devel_yandell-lab.org
> 
> 
> 
> -- 
> Getiria Onsongo, Ph.D.
> Informatics Analyst, Research Informatics Support System
> Minnesota Supercomputing Institute for Advanced Computational Research
> University of Minnesota
> Minneapolis, MN 55455
> Phone: 612-624-0532 <tel:612-624-0532>



-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532


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