[maker-devel] duplicate exons?

[Uma Maheswari]

Hi Carson,

I checked with Michael, this is different from what he saw, he had 
entire segements of gff files duplicated, In this case, just Parent id is.
I am preparing the files you asked for, will send them soon

thanks
Uma


On 16/05/13 17:50, Carson Holt wrote:
> Yes. Perhaps this is the same issue Michael saw, although the one 
> difference I see from his post is the Parent= attribute.
>
> --> 
> Parent=augustus_masked-3-processed-gene-6.179-mRNA-1,augustus_masked-3-processed-gene-6.179-mRNA-1
>
> I have seen duplicate exons from GFF3 pass-through in the past, but if 
> that's not being used I'd be very appreciative of any test dataset you 
> could give me.
>
> Thanks,
> Carson
>
>
>
>
> From: Daniel Hughes <dsth at ebi.ac.uk <mailto:dsth at ebi.ac.uk>>
> Date: Thursday, 16 May, 2013 12:38 PM
> To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Cc: Uma Maheswari <uma at ebi.ac.uk <mailto:uma at ebi.ac.uk>>, 
> "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" 
> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: Re: [maker-devel] duplicate exons?
>
> hiya, are you using the same instance as michael at ebi as this sounds 
> like the same problem he had last week and he wasn't running pass 
> through. i've run 2.27 here 30+ times here and not seen this? is 
> something very strange corrupted?
>
> dan.
>
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
> -------------------------------------------------------------------------------------
> dsth at cantab.net <mailto:dsth at cantab.net>
> dsth at cpan.org <mailto:dsth at cpan.org>
>
>
> 2013/5/16 Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
>
>     I think this also may be a result of using GFF3 pass-through.  So
>     if that
>     is the case, could you send me any GFF3 files you gave maker in
>     addition
>     to the other files I asked for.
>
>     Thanks,
>     Carson
>
>
>
>     On 13-05-16 12:08 PM, "Uma Maheswari" <uma at ebi.ac.uk
>     <mailto:uma at ebi.ac.uk>> wrote:
>
>     >Hi Carson,
>     >
>     >When I was trying to load the Maker-2.27 results into ensembl, I found
>     >that few hundreds of genes with 'duplicate exons' . When I looked
>     in the
>     >gff file, I found cases like this, where the exons are not actually
>     >duplicated but have two Parents with same mRNA ID. This can be a
>     >potential alternate transcript, attached to the same transcript by
>     >mistake?
>     >
>     >Many thanks
>     >Uma
>     >
>     >
>     >
>     >
>     >
>     >3       maker   gene    524271  525467  .       -       .
>     >ID=augustus_masked-3-processed-gene-6.179;Name=augustus_masked-3-processed
>     >-gene-6.179
>     >3       maker   mRNA    524271  525467  .       -       .
>     >ID=augustus_masked-3-processed-gene-6.179-mRNA-1;Parent=augustus_masked-3-
>     >processed-gene-6.179;Name=augustus_masked-3-processed-gene-6.179-mRNA-1;_A
>     >ED=0.50;_eAED=0.63;_QI=1476|0.33|0.75|1|0|0.25|4|0|406
>     >3       maker   exon    524271  524480  .       -       .
>     >ID=augustus_masked-3-processed-gene-6.179-mRNA-1:exon:573;Parent=augustus_
>     >masked-3-processed-gene-6.179-mRNA-1
>     >3       maker   exon    524538  525182  .       -       .
>     >ID=augustus_masked-3-processed-gene-6.179-mRNA-1:exon:572;Parent=augustus_
>     >masked-3-processed-gene-6.179-mRNA-1,augustus_masked-3-processed-gene-6.17
>     >9-mRNA-1
>     >3       maker   exon    524271  525467  .       -       .
>     >ID=augustus_masked-3-processed-gene-6.179-mRNA-1:exon:571;Parent=augustus_
>     >masked-3-processed-gene-6.179-mRNA-1
>     >3       maker   CDS     524538  524903  .       -       0
>     >ID=augustus_masked-3-processed-gene-6.179-mRNA-1:cds;Parent=augustus_maske
>     >d-3-processed-gene-6.179-mRNA-1
>     >3       maker   CDS     524538  525182  .       -       0
>     >ID=augustus_masked-3-processed-gene-6.179-mRNA-1:cds;Parent=augustus_maske
>     >d-3-processed-gene-6.179-mRNA-1
>     >3       maker   CDS     524271  524480  .       -       0
>     >ID=augustus_masked-3-processed-gene-6.179-mRNA-1:cds;Parent=augustus_maske
>     >d-3-processed-gene-6.179-mRNA-1
>     >3       maker   five_prime_UTR  524271  525467  .       -       .
>     >ID=augustus_masked-3-processed-gene-6.179-mRNA-1:five_prime_utr;Parent=aug
>     >ustus_masked-3-processed-gene-6.179-mRNA-1
>     >3       maker   five_prime_UTR  524904  525182  .       -       .
>     >ID=augustus_masked-3-processed-gene-6.179-mRNA-1:five_prime_utr;Parent=aug
>     >ustus_masked-3-processed-gene-6.179-mRNA-1
>     >
>     >
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