[maker-devel] Maker exon number

[Carson Holt]

I can do that.  Just a note of caution though.  The ID= attribute is not
protected (it's just an identifier to relate things to one another for
correct parentage).  Downstream scripts that use or manipulate GFF3 files
can change it (so relying on it to always be the same or even be informative
is not guaranteed).

--Carson


From:  Guohong Cai <caigh02 at gmail.com>
Date:  Monday, May 19, 2014 at 9:43 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker exon number

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-g
ene-0.0
scaffold1       maker   mRNA    106     2985    .       +       .
ID=genemark-scaffold1-processed-gene-0.0-mRNA-1;Parent=genemark-scaffold1-pr
ocessed-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-scaff
old1-processed-gene-0.0-mRNA-1
scaffold1       maker   exon    1878    2440    .       +       .
ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:exon:1;Parent=genemark-scaff
old1-processed-gene-0.0-mRNA-1
scaffold1       maker   exon    2605    2985    .       +       .
ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:exon:2;Parent=genemark-scaff
old1-processed-gene-0.0-mRNA-1
scaffold1       maker   CDS     106     1684    .       +       0
ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:cds;Parent=genemark-scaffold
1-processed-gene-0.0-mRNA-1
scaffold1       maker   CDS     1878    2440    .       +       2
ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:cds;Parent=genemark-scaffold
1-processed-gene-0.0-mRNA-1
scaffold1       maker   CDS     2605    2985    .       +       0
ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:cds;Parent=genemark-scaffold
1-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-ge
ne-0.254-mRNA-1
scaffold1       maker   CDS     38616   38742   .       +       2
ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-ge
ne-0.254-mRNA-1
scaffold1       maker   CDS     38831   39986   .       +       1
ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-ge
ne-0.254-mRNA-1
scaffold1       maker   CDS     40073   40154   .       +       0
ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-ge
ne-0.254-mRNA-1
scaffold1       maker   CDS     40259   40666   .       +       2
ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-ge
ne-0.254-mRNA-1
scaffold1       maker   CDS     40745   41604   .       +       2
ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-ge
ne-0.254-mRNA-1

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