[maker-devel] Duplicated exons

[Michael Nuhn]

On 05/10/2013 05:25 PM, Carson Holt wrote:
> Very odd.  Which version of MAEKR are you using.  Are you using GFF3
> passthrough in the run that generates the duplication?

I am using version 2.27 of maker. I am not using the passthrough option.

Cheers,
Michael.

> 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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>
>