[maker-devel] Duplicated exons

[Carson Holt]

Very odd.  Which version of MAEKR are you using.  Are you using GFF3
passthrough in the run that generates the duplication?

Thanks,
Carson


On 13-05-10 8:10 AM, "Michael Nuhn" <mnuhn at ebi.ac.uk> wrote:

>Hello Carson!
>
>I have been trying to get to the bottom of an error message when
>(re)training snap. Snap, or more precisely fathom, was giving me unclear
>error messages about misordered and overlapping exons.
>
>I have looked into the gff files from which these exons originate and
>noticed that a lot of exons in that file were duplicated. For example I
>have found these:
>
>LSalAtl2s75	maker	exon	186317	186936	.	+	.
>ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:3;Parent=maker-LSalAtl2s75
>-snap-gene-2.15-mRNA-1
>LSalAtl2s75	maker	exon	187007	191531	.	+	.
>ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:4;Parent=maker-LSalAtl2s75
>-snap-gene-2.15-mRNA-1
>
>and then about four hundred lines later there are these:
>
>LSalAtl2s75	maker	exon	186317	186936	.	+	.
>ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:1;Parent=maker-LSalAtl2s75
>-snap-gene-2.15-mRNA-1
>LSalAtl2s75	maker	exon	187007	191531	.	+	.
>ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:2;Parent=maker-LSalAtl2s75
>-snap-gene-2.15-mRNA-1
>
>which are identical except for the order number after "exon:".
>
>This seems to have happened to a lot of features in that file.
>
>How can I avoid this? Or if this is just a rare problem, can I have
>maker recompute the gff file without redoing all the computations again?
>
>Cheers,
>Michael.
>
>
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