[maker-devel] Maker: accessory scripts

[Carson Holt]

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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