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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">After running my rounds with Maker, I went on to using the Genome Annotation Generator (GAG) and tbl2asn to find errors and fix them. My plan is to run BLAST and InterProScan after so that I don’t waste time annotating invalid features.
However, when running GAG, all the protein_gff:protein2genome annotations get removed, along with the Name matches that I got to related species. Somehow I feel it would be better to find the errors, and go back to the last Maker generated gff3 instead of
continuing on successively with each GAG-cleaned-up gff. However, another thing is that the start and stop codons are not included in the Maker gff, and there is no way that I can fix this all in the original manually.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">My question is, is it a real loss to lose the protein_gff:protein2genome information, and all the Name info, or does this get added back once I run BLAST and InterProScan? Does Maker have a function to add the Start and Stop codons? Should
I really be running BLAST and InterProScan before going on to GAG? Lastly, MAKER adds tRNA annotations, but for each of these, tbl2asn results in errors: SEQ_FEAT.MissingTrnaAA, and I’m not sure if I can just ignore this…<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Emily<span style="mso-fareast-language:EN-CA"> </span><span style="font-size:8.0pt;color:black;mso-fareast-language:EN-CA"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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