[maker-devel] duplicate CDS in annotation

[Sasha Mikheyev]

Hi Carson,

I have been using version 2.10. Is it worth trying with a newer version?

You can find the model file here<https://dl.dropbox.com/u/5275622/all.gff.gz>.
It is rather large, as it includes all of the output from the first maker
run.

Yours,

Sasha


On Mon, Mar 11, 2013 at 10:02 PM, Carson Holt <carsonhh at gmail.com> wrote:

> I think the issue is that you are getting a match feature that is being
> printed with the same ID as the mRNA feature. Correct?
>
> What version of MAKER are you using, and what does the gile you are giving
> to pred_gff or model_gff look like?  Could you send them?
>
> Thanks,
> Carson
>
>
> From: Barry Moore <barry.moore at genetics.utah.edu>
> Date: Monday, 11 March, 2013 7:32 AM
> To: Sasha Mikheyev <mikheyev at gmail.com>
> Cc: <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] duplicate CDS in annotation
>
> Hi Sasha,
>
> This gene model appears to be correctly formatted to me.  In GFF3 format
> the CDS features are allowed to span multiple lines and they share the same
> ID to indicate that it is all the same features.  See the GFF3
> specification on the Sequence Ontology website (
> http://www.sequenceontology.org/resources/gff3.html), and in particular
> the description of the ID attribute specifies:
>
> ID Indicates the ID of the feature. IDs for each feature must be unique
> within the scope of the GFF file. In the case of discontinuous features
> (i.e. a single feature that exists over multiple genomic locations) the
> same ID may appear on multiple lines. All lines that share an ID
> collectively represent a single feature.
>
>
> So each of those CDS lines forms one part of the single CDS feature for
> this gene.
>
> B
>
> On Mar 11, 2013, at 3:46 AM, Sasha Mikheyev wrote:
>
> Dear Yandell lab,
>
> I am re-annotating the harvester and genome using protein and RNA-seq
> data. However, I get many artifacts like the one below. It seems that there
> are several CDS records that should tie in to the same mRNA, but they are
> really hanging out separately, and produce several nucleotide sequences
> with the same name when extracted from the gff. I would appreciate any
> guidance about how to fix this!
>
> Thank you,
>
> Sasha
>
> grep "pbar_scf7180000350377:hit:2506" Pbar.2.0.gff
> pbar_scf7180000350377 protein2genome protein_match 172004 172162 150 - .
> ID=pbar_scf7180000350377:hit:2506;Name=Hsal|HS9704;score=150;
> pbar_scf7180000350377 protein2genome match_part 172004 172162 150 - . ID=pbar_scf7180000350377:hsp:2798;Parent=pbar_scf7180000350377:hit:2506;Name=Hsal|HS9704;Target=Hsal|HS9704
> 1 53 +;Gap=M159;
> pbar_scf7180000350377 maker mRNA 538308 558769 . + .
> ID=pbar_scf7180000350377:hit:2506;Parent=augustus_masked-pbar_scf7180000350377-abinit-gene-5.29;Name=augustus_masked-pbar_scf7180000350377-abinit-gene-5.29-mRNA-1;_AED=0.48;_eAED=0.39;_QI=0|0|0|0.5|1|1|6|0|395;score=0.01;
> pbar_scf7180000350377 maker exon 538308 538334 0.01 + .
> ID=pbar_scf7180000350377:hit:2506:exon:305;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377 maker exon 538748 538968 0.01 + .
> ID=pbar_scf7180000350377:hit:2506:exon:306;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377 maker exon 539842 540242 0.01 + .
> ID=pbar_scf7180000350377:hit:2506:exon:307;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377 maker exon 542624 542798 0.01 + .
> ID=pbar_scf7180000350377:hit:2506:exon:308;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377 maker exon 555823 556025 0.01 + .
> ID=pbar_scf7180000350377:hit:2506:exon:309;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377 maker exon 558609 558769 0.01 + .
> ID=pbar_scf7180000350377:hit:2506:exon:310;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377 maker CDS 538308 538334 . + 0
> ID=pbar_scf7180000350377:hit:2506:cds:305;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377 maker CDS 538748 538968 . + 0
> ID=pbar_scf7180000350377:hit:2506:cds:306;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377 maker CDS 539842 540242 . + 1
> ID=pbar_scf7180000350377:hit:2506:cds:307;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377 maker CDS 542624 542798 . + 2
> ID=pbar_scf7180000350377:hit:2506:cds:308;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377 maker CDS 555823 556025 . + 1
> ID=pbar_scf7180000350377:hit:2506:cds:309;Parent=pbar_scf7180000350377:hit:2506;
> pbar_scf7180000350377 maker CDS 558609 558769 . + 2
> ID=pbar_scf7180000350377:hit:2506:cds:310;Parent=pbar_scf7180000350377:hit:2506;
>
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>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
>
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