[maker-devel] duplicate exons?

Uma Maheswari uma at ebi.ac.uk
Tue May 28 06:00:54 MDT 2013 

Thanks Carson,

2.28 with -a command line flag fixed this problem.

Uma
On 17/05/13 09:41, Uma Maheswari wrote:
> 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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