[maker-devel] Maker: accessory scripts

[Daniel Ence]

Hi Innocent, I'm just jumping in this conversation kind of late in the game, but if you look in the gff3 file that maker gave you, do you see any gene, exon, or CDS features in the output? When you give evidence (protein or EST) and ab-initio predictors to maker the default behavior is to create gene models.

Thanks,
Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________
From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Innocent Onsongo [onson001 at umn.edu]
Sent: Wednesday, June 05, 2013 10:35 AM
To: Carson Holt
Cc: maker-devel at yandell-lab.org; Barry Moore
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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