[maker-devel] Maker exon number

[Guohong Cai]

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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