[maker-devel] Maker: accessory scripts

[Innocent Onsongo]

Thanks for the timely feedback Carson. I made a change to my pred_gff
and est_gff GFF3 files and now I am getting results but I am not sure if
the changes I made are valid. I want to make sure the changes I made did
not lead Maker to behave in an unexpected way and lead to results that
might be incorrect.

In my pred_gff file, I replaced "mRNA" with "protein_match" and "exon" with
"match" below are the first three lines of the old and new pred_gff files
respectively

---------------old pred_gff
##gff-version 3
CGS00003        AUGUSTUS        mRNA    1       10865   1       +       .

CGS00003        AUGUSTUS        exon    2013    2050    .       +       1


---------------new pred_gff
##gff-version 3
CGS00003        AUGUSTUS        protein_match   1       10865   1       +
    .
CGS00003        AUGUSTUS        match_part      2013    2050    .       +
    1

In my est_gff file, I replaced "mRNA" with "protein_match" and "exon" with
"match" below are the first three lines of the old and new pred_gff files
respectively

----------------old est_gff
##gff-version 3
CGS00003        EST_BLAT        mRNA    4641336 4758501 6072    -       .

CGS00003        EST_BLAT        exon    4641336 4641979 644     -       .


----------------new est_gff
CGS00003 EST_BLAT expressed_sequence_match 4641336 4758501 6072 - .
CGS00003 EST_BLAT match_part 4641336 4641979 644 - .

Are the changes I made valid?

Thanks,
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
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>



-- 
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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