<div>Dear Yandell lab,</div><div><br></div><div>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!</div>

<div><br></div><div>Thank you,</div><div><br></div><div>Sasha</div><div><br></div><div>grep "pbar_scf7180000350377:hit:2506" Pbar.2.0.gff </div><div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre">     </span>protein2genome<span class="Apple-tab-span" style="white-space:pre">      </span>protein_match<span class="Apple-tab-span" style="white-space:pre">       </span>172004<span class="Apple-tab-span" style="white-space:pre">      </span>172162<span class="Apple-tab-span" style="white-space:pre">      </span>150<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre">   </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>ID=pbar_scf7180000350377:hit:2506;Name=Hsal|HS9704;score=150;</div>

<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>protein2genome<span class="Apple-tab-span" style="white-space:pre">      </span>match_part<span class="Apple-tab-span" style="white-space:pre">  </span>172004<span class="Apple-tab-span" style="white-space:pre">      </span>172162<span class="Apple-tab-span" style="white-space:pre">      </span>150<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre">   </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>ID=pbar_scf7180000350377:hsp:2798;Parent=pbar_scf7180000350377:hit:2506;Name=Hsal|HS9704;Target=Hsal|HS9704 1 53 +;Gap=M159;</div>

<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">       </span>mRNA<span class="Apple-tab-span" style="white-space:pre">        </span>538308<span class="Apple-tab-span" style="white-space:pre">      </span>558769<span class="Apple-tab-span" style="white-space:pre">      </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>+<span class="Apple-tab-span" style="white-space:pre">   </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>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;</div>

<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">       </span>exon<span class="Apple-tab-span" style="white-space:pre">        </span>538308<span class="Apple-tab-span" style="white-space:pre">      </span>538334<span class="Apple-tab-span" style="white-space:pre">      </span>0.01<span class="Apple-tab-span" style="white-space:pre">        </span>+<span class="Apple-tab-span" style="white-space:pre">   </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>ID=pbar_scf7180000350377:hit:2506:exon:305;Parent=pbar_scf7180000350377:hit:2506;</div>

<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">       </span>exon<span class="Apple-tab-span" style="white-space:pre">        </span>538748<span class="Apple-tab-span" style="white-space:pre">      </span>538968<span class="Apple-tab-span" style="white-space:pre">      </span>0.01<span class="Apple-tab-span" style="white-space:pre">        </span>+<span class="Apple-tab-span" style="white-space:pre">   </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>ID=pbar_scf7180000350377:hit:2506:exon:306;Parent=pbar_scf7180000350377:hit:2506;</div>

<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">       </span>exon<span class="Apple-tab-span" style="white-space:pre">        </span>539842<span class="Apple-tab-span" style="white-space:pre">      </span>540242<span class="Apple-tab-span" style="white-space:pre">      </span>0.01<span class="Apple-tab-span" style="white-space:pre">        </span>+<span class="Apple-tab-span" style="white-space:pre">   </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>ID=pbar_scf7180000350377:hit:2506:exon:307;Parent=pbar_scf7180000350377:hit:2506;</div>

<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">       </span>exon<span class="Apple-tab-span" style="white-space:pre">        </span>542624<span class="Apple-tab-span" style="white-space:pre">      </span>542798<span class="Apple-tab-span" style="white-space:pre">      </span>0.01<span class="Apple-tab-span" style="white-space:pre">        </span>+<span class="Apple-tab-span" style="white-space:pre">   </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>ID=pbar_scf7180000350377:hit:2506:exon:308;Parent=pbar_scf7180000350377:hit:2506;</div>

<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">       </span>exon<span class="Apple-tab-span" style="white-space:pre">        </span>555823<span class="Apple-tab-span" style="white-space:pre">      </span>556025<span class="Apple-tab-span" style="white-space:pre">      </span>0.01<span class="Apple-tab-span" style="white-space:pre">        </span>+<span class="Apple-tab-span" style="white-space:pre">   </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>ID=pbar_scf7180000350377:hit:2506:exon:309;Parent=pbar_scf7180000350377:hit:2506;</div>

<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">       </span>exon<span class="Apple-tab-span" style="white-space:pre">        </span>558609<span class="Apple-tab-span" style="white-space:pre">      </span>558769<span class="Apple-tab-span" style="white-space:pre">      </span>0.01<span class="Apple-tab-span" style="white-space:pre">        </span>+<span class="Apple-tab-span" style="white-space:pre">   </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>ID=pbar_scf7180000350377:hit:2506:exon:310;Parent=pbar_scf7180000350377:hit:2506;</div>

<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">       </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>538308<span class="Apple-tab-span" style="white-space:pre">      </span>538334<span class="Apple-tab-span" style="white-space:pre">      </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>+<span class="Apple-tab-span" style="white-space:pre">   </span>0<span class="Apple-tab-span" style="white-space:pre">   </span>ID=pbar_scf7180000350377:hit:2506:cds:305;Parent=pbar_scf7180000350377:hit:2506;</div>

<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">       </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>538748<span class="Apple-tab-span" style="white-space:pre">      </span>538968<span class="Apple-tab-span" style="white-space:pre">      </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>+<span class="Apple-tab-span" style="white-space:pre">   </span>0<span class="Apple-tab-span" style="white-space:pre">   </span>ID=pbar_scf7180000350377:hit:2506:cds:306;Parent=pbar_scf7180000350377:hit:2506;</div>

<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">       </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>539842<span class="Apple-tab-span" style="white-space:pre">      </span>540242<span class="Apple-tab-span" style="white-space:pre">      </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>+<span class="Apple-tab-span" style="white-space:pre">   </span>1<span class="Apple-tab-span" style="white-space:pre">   </span>ID=pbar_scf7180000350377:hit:2506:cds:307;Parent=pbar_scf7180000350377:hit:2506;</div>

<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">       </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>542624<span class="Apple-tab-span" style="white-space:pre">      </span>542798<span class="Apple-tab-span" style="white-space:pre">      </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>+<span class="Apple-tab-span" style="white-space:pre">   </span>2<span class="Apple-tab-span" style="white-space:pre">   </span>ID=pbar_scf7180000350377:hit:2506:cds:308;Parent=pbar_scf7180000350377:hit:2506;</div>

<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">       </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>555823<span class="Apple-tab-span" style="white-space:pre">      </span>556025<span class="Apple-tab-span" style="white-space:pre">      </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>+<span class="Apple-tab-span" style="white-space:pre">   </span>1<span class="Apple-tab-span" style="white-space:pre">   </span>ID=pbar_scf7180000350377:hit:2506:cds:309;Parent=pbar_scf7180000350377:hit:2506;</div>

<div>pbar_scf7180000350377<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre">       </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>558609<span class="Apple-tab-span" style="white-space:pre">      </span>558769<span class="Apple-tab-span" style="white-space:pre">      </span>.<span class="Apple-tab-span" style="white-space:pre">   </span>+<span class="Apple-tab-span" style="white-space:pre">   </span>2<span class="Apple-tab-span" style="white-space:pre">   </span>ID=pbar_scf7180000350377:hit:2506:cds:310;Parent=pbar_scf7180000350377:hit:2506;</div>

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