[maker-devel] Duplicated exons

[Michael Nuhn]

On 05/10/2013 07:08 PM, Carson Holt wrote:
> 2.27 from the website download or the SVN devel version?

SVN. I checked it out on 19/03/2013.

> Thanks,
> Carson
>
>
> On 13-05-10 1:35 PM, "Michael Nuhn" <mnuhn at ebi.ac.uk> wrote:
>
>> 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-LSalAtl2s
>>>> 75
>>>> -snap-gene-2.15-mRNA-1
>>>> LSalAtl2s75	maker	exon	187007	191531	.	+	.
>>>>
>>>> ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:4;Parent=maker-LSalAtl2s
>>>> 75
>>>> -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-LSalAtl2s
>>>> 75
>>>> -snap-gene-2.15-mRNA-1
>>>> LSalAtl2s75	maker	exon	187007	191531	.	+	.
>>>>
>>>> ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:2;Parent=maker-LSalAtl2s
>>>> 75
>>>> -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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>>>
>>>
>>
>
>