[maker-devel] duplicate exons?

[Carson Holt]

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-proce
ssed-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>
Date:  Thursday, 16 May, 2013 12:38 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Uma Maheswari <uma at ebi.ac.uk>, "maker-devel at yandell-lab.org"
<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
dsth at cpan.org


2013/5/16 Carson Holt <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> 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
>> >
>> >
>> >_______________________________________________
>> >maker-devel mailing list
>> >maker-devel at box290.bluehost.com
>> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 
> 
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