[maker-devel] Maker: accessory scripts

Fri Jun 7 20:29:50 MDT 2013

I appreciate the feedback. I will try letting MAKER run augustus instead of
passing the Augustus predictions as GFF3.

Thanks for all you help!

Getiria

On Fri, Jun 7, 2013 at 5:10 PM, Carson Holt <carsonhh at gmail.com> wrote:

> 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
> …/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.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
>

-- 
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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