[maker-devel] duplicate exons?

[Carson Holt]

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
>
>
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