[maker-devel] Duplicated exons

[Daniel Hughes]

That is odd. i've run that version of maker 30-40x at ebi lately and never
seen it. Is it just one scaffold? While i'd be surprised if it's the cause
but have you been playing with the file locking options Carson mentioned a
while back? I'd definitely be inclined to re-process it if it's just the
one scaffold.

Dan
On May 10, 2013 12:45 PM, "Michael Nuhn" <mnuhn at ebi.ac.uk> wrote:
>
> Hello Carson!
>
> I have been trying to get to the bottom of an error message when
(re)training snap. Snap, or more precisely fathom, was giving me unclear
error messages about misordered and overlapping exons.
>
> I have looked into the gff files from which these exons originate and
noticed that a lot of exons in that file were duplicated. For example I
have found these:
>
> LSalAtl2s75     maker   exon    186317  186936  .       +       .
ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:3;Parent=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1
> LSalAtl2s75     maker   exon    187007  191531  .       +       .
ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:4;Parent=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1
>
> and then about four hundred lines later there are these:
>
> LSalAtl2s75     maker   exon    186317  186936  .       +       .
ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:1;Parent=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1
> LSalAtl2s75     maker   exon    187007  191531  .       +       .
ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:2;Parent=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1
>
> which are identical except for the order number after "exon:".
>
> This seems to have happened to a lot of features in that file.
>
> How can I avoid this? Or if this is just a rare problem, can I have maker
recompute the gff file without redoing all the computations again?
>
> Cheers,
> Michael.
>
>
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