[maker-devel] Maker exon number
Guohong Cai
caigh02 at gmail.com
Wed May 21 08:40:47 MDT 2014
Thanks a lot.---Guohong
On Tue, May 20, 2014 at 7:52 PM, Carson Holt <carsonhh at gmail.com> wrote:
> 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-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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