[maker-devel] duplicate exons?

[Carson Holt]

I've had one other report of this on the devel list, but haven't gotten
data to test with.  Do you have the run files that produced the duplicate
exon?

If so, cCould you send me theVoid directory for the contig that shows the
dulicate, and the maker_opts.ctl file?

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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