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<p class="MsoNormal">Dear maker team,</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am writing to ask for your help. </p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am using make to annotate a big genome ~9 Gbp, I have 3 evidences: 1) Transcriptome of this species; 2) protein sequence from relative species; 3) Augustus model trained from pasa.
</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">When I use all of these 3 evidences to annotate the genome (basic pipeline), the distribution of AED score is weird (single peak around 0.5).
</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have also tried to update the gene model I got from pasa using maker, the distribution of AED scores is the same.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">But when I try to only use EST or protein as evidence (est2genome or protein2genome), the AED scores is normal (close to 0).
</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">To my understand, it seems all the 3 evidences are conflict with each other, results in the AED scores is higher (~ 0.5) than expected, could you give me some suggestion on how to fix this problem?</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best regards,</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Wei</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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