[maker-devel] duplicate CDS in annotation

[Sasha Mikheyev]

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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