[maker-devel] exon numbering bug?

[Carson Holt]

There has been some post processing of the GFF3.  It is not an original
MAKER result file.  I can tell based on the ID's (maker doesn't assign
numerical IDs).

Most likely it was processed to make exons unique without having dual
parentage.  Normally if the same exon is found in two transcripts it will
have two parents separated by a comma.  I imaging that the post processing
script duplicated the exon, creating independent IDs and split the parents,
but left the Name= tag the same.  Since the Name= tag was based off of the
first transcript the exon belonged to, it stayed the same.

--Carson



From:  "Kang, Yang Jae" <kangyangjae at gmail.com>
Date:  Sunday, 12 May, 2013 11:53 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] exon numbering bug?

Hello
 
I want to check this is bug or my misunderstanding. The following is the
gff3 result of maker pipeline.
I think those red marks should be mRNA-2. This type of error was found only
at exon
 
scaffold_22        maker   mRNA   604856  612126  .          +         .
ID=211342;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2;Parent=211320
scaffold_22        maker   exon     604856  605185  0.51      +         .
ID=211343;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2788;Parent
=211342
scaffold_22        maker   exon     608362  608456  0.51      +         .
ID=211344;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2791;Parent
=211342
scaffold_22        maker   exon     610193  610286  0.51      +         .
ID=211345;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2792;Parent
=211342
scaffold_22        maker   exon     610583  610714  0.51      +         .
ID=211346;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2793;Parent
=211342
scaffold_22        maker   exon     610838  610942  0.51      +         .
ID=211347;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2794;Parent
=211342
scaffold_22        maker   exon     611458  612126  0.51      +         .
ID=211348;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2795;Parent
=211342
scaffold_22        maker   five_prime_UTR   604856  604972  .          +
.          
ID=211349;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:UTR1;Parent=2113
42
scaffold_22        maker   CDS      604973  605185  .          +         0
ID=211350;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2905;Parent=
211342
scaffold_22        maker   CDS      608362  608456  .          +         0
ID=211351;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2906;Parent=
211342
scaffold_22        maker   CDS      610193  610286  .          +         1
ID=211352;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2907;Parent=
211342
scaffold_22        maker   CDS      610583  610714  .          +         0
ID=211353;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2908;Parent=
211342
scaffold_22        maker   CDS      610838  610942  .          +         0
ID=211354;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2909;Parent=
211342
scaffold_22        maker   CDS      611458  611661  .          +         0
ID=211355;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2910;Parent=
211342
scaffold_22        maker   three_prime_UTR 611662  612126  .          +
.          
ID=211356;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:UTR2;Parent=2113
42
scaffold_22        maker   start_codon       604973  604975  .          +
.          
ID=211357;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:start1;Parent=21
1342
scaffold_22        maker   stop_codon       611659  611661  .          +
.          
ID=211358;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:stop2;Parent=211
342
 
Thank you!
 
Kang, Yang Jae 
Ph.D.
Cropgenomics Lab.
College of Agriculture and Life Science
Seoul National University
Korea
 
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