[maker-devel] Maker exon number

[Carson Holt]

I've gone ahead and made the change in the devlopment version.   It will
probably be convenient in most cases, but it's important to note one caveat.
Exon features are shared in GFF3 format.  So if there are multiple isoforms
that contain the same exon, there will only be a single exon line in the
GFF3, but it will list several transcript IDs in it's Parent= attribute.

What does that have to do with with the ID= attribute or exon order?  Well
it means that ID=exon:2 in the first transcript may be the second exon, but
in another transcript ID=exon:2 may be the first exon or third exon, etc.
This is because there is only a single line for a given exon and it gets
shared by all the transcripts.  So it will always have the same ID= tag, but
will hold a different position in different isoforms (so it's ordinal value
will not go along with the ID in those cases).  But since most gene calls
from MAKER will have only one isoform (default) it could still be convenient
in those cases.

Thanks,
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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