[maker-devel] Maker: accessory scripts

[Innocent Onsongo]

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.com
>> http://box290.bluehost.com/mailman/listinfo/maker-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
>



-- 
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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