Re: [maker-devel] duplicate exons?

[Uma Maheswari]

Hi Carson,

I checked with Michael, this is different from what he saw, he had entire segements of gff files duplicated, In this case, just Parent id is.
I am preparing the files you asked for, will send them soon

thanks
Uma


On 16/05/13 17:50, Carson Holt wrote:

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-processed-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 <ds...@ebi.ac.uk>
Date: Thursday, 16 May, 2013 12:38 PM
To: Carson Holt <cars...@gmail.com>
Cc: Uma Maheswari <u...@ebi.ac.uk>, "maker...@yandell-lab.org" <maker...@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)
-------------------------------------------------------------------------------------
ds...@cantab.net
ds...@cpan.org

2013/5/16 Carson Holt <cars...@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" <u...@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...@box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



_______________________________________________
maker-devel mailing list
maker...@box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

[Uma Maheswari]

Thanks Carson,

2.28 with -a command line flag fixed this problem.

Uma