[maker-devel] Duplicated exons

[Carson Holt]

2.27 from the website download or the SVN devel version?

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.
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>