[maker-devel] Maker: accessory scripts

[Carson Holt]

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
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> er-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


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