[maker-devel] Maker exon number

[Guohong Cai]

Hi Daniel, I am using maker-2.31.5.---Guohong


On Tue, May 20, 2014 at 3:34 PM, Daniel Ence <dence at genetics.utah.edu>wrote:

> Hi Guohong,
>
> What version of MAKER are you running?
>
> Thanks,
> Daniel
>
>
> On May 19, 2014, at 9:43 PM, Guohong Cai <caigh02 at gmail.com>
>  wrote:
>
> > Hi Carson,
> >
> > I am using MAKER to annotate a few small genomes. When looking through
> the gff file, I notice that the exon numbers do not start from 0 or 1 for
> each gene. Only the first gene in a scaffold start with exon 0. If the
> first gene has 3 exons (0-2), then the second gene will start from exon 3
> (an example is shown below). It seems many people would prefer that in each
> gene, the first exon be exon 1. Is it possible to make such a change?
>  Thanks.
> >
> > Guohong
> >
> >
> > scaffold1       .       contig  1       347483  .       .       .
> ID=scaffold1;Name=scaffold1
> > scaffold1       maker   gene    106     2985    .       +       .
> ID=genemark-scaffold1-processed-gene-0.0;Name=genemark-scaffold1-processed-gene-0.0
> > scaffold1       maker   mRNA    106     2985    .       +       .
> ID=genemark-scaffold1-processed-gene-0.0-mRNA-1;Parent=genemark-scaffold1-processed-gene-0.0;Name=genemark-scaffold1-processed-gene-0.0-mRNA-1;_AED=0.12;_eAED=0.13;_QI=0|0|0|1|1|1|3|0|840
> > scaffold1       maker   exon    106     1684    .       +       .
> ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:exon:0;Parent=genemark-scaffold1-processed-gene-0.0-mRNA-1
> > scaffold1       maker   exon    1878    2440    .       +       .
> ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:exon:1;Parent=genemark-scaffold1-processed-gene-0.0-mRNA-1
> > scaffold1       maker   exon    2605    2985    .       +       .
> ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:exon:2;Parent=genemark-scaffold1-processed-gene-0.0-mRNA-1
> > scaffold1       maker   CDS     106     1684    .       +       0
> ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:cds;Parent=genemark-scaffold1-processed-gene-0.0-mRNA-1
> > scaffold1       maker   CDS     1878    2440    .       +       2
> ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:cds;Parent=genemark-scaffold1-processed-gene-0.0-mRNA-1
> > scaffold1       maker   CDS     2605    2985    .       +       0
> ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:cds;Parent=genemark-scaffold1-processed-gene-0.0-mRNA-1
> > scaffold1       maker   gene    38466   41604   .       +       .
> ID=maker-scaffold1-snap-gene-0.254;Name=maker-scaffold1-snap-gene-0.254
> > scaffold1       maker   mRNA    38466   41604   .       +       .
> ID=maker-scaffold1-snap-gene-0.254-mRNA-1;Parent=maker-scaffold1-snap-gene-0.254;Name=maker-scaffold1-snap-gene-0.254-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|0|0|0.83|1|1|6|0|892
> > scaffold1       maker   exon    38466   38511   .       +       .
> ID=maker-scaffold1-snap-gene-0.254-mRNA-1:exon:3;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1
> > scaffold1       maker   exon    38616   38742   .       +       .
> ID=maker-scaffold1-snap-gene-0.254-mRNA-1:exon:4;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1
> > scaffold1       maker   exon    38831   39986   .       +       .
> ID=maker-scaffold1-snap-gene-0.254-mRNA-1:exon:5;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1
> > scaffold1       maker   exon    40073   40154   .       +       .
> ID=maker-scaffold1-snap-gene-0.254-mRNA-1:exon:6;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1
> > scaffold1       maker   exon    40259   40666   .       +       .
> ID=maker-scaffold1-snap-gene-0.254-mRNA-1:exon:7;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1
> > scaffold1       maker   exon    40745   41604   .       +       .
> ID=maker-scaffold1-snap-gene-0.254-mRNA-1:exon:8;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1
> > scaffold1       maker   CDS     38466   38511   .       +       0
> ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1
> > scaffold1       maker   CDS     38616   38742   .       +       2
> ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1
> > scaffold1       maker   CDS     38831   39986   .       +       1
> ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1
> > scaffold1       maker   CDS     40073   40154   .       +       0
> ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1
> > scaffold1       maker   CDS     40259   40666   .       +       2
> ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1
> > scaffold1       maker   CDS     40745   41604   .       +       2
> ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1
> >
> > _______________________________________________
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>
>
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