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<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div><div>Hello MAKER team,</div><div><br></div><div>We at JCVI have been using MAKER (2.31.8) to calculate the AED of Arabidopsis gene models. We provided the annotation set as ‘model_gff’ with evidence file in ‘protein_gff’ and ‘est_gff’. All the other settings were default. One issue I’ve noticed was that the AED scores did not seem to be deterministic. When I compare the AED scores from two runs using identical control files, ~1,000 (out of 35,385) gene models had different AED scores. The difference between two sets of AED scores could range from 0.01 to 1.00.</div><div><br></div><div>I looked into several gene models with lager difference, i.e. AED = 0.00 in run 1 and AED = 1.00 in run 2, and noticed a disagreement in the QI:</div><div><br></div><div>Run 1: _AED=0.00;_eAED=-0.00;_QI=0|-1|0|1|-1|0|1|0|344</div><div>Run 2: _AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|0|344</div><div><br></div><div>The discrepancy in the 4th column seemed to suggest the evidence file was not used properly in run 2. I’m not sure what may have caused as both runs have used the same input. A snapshot of the evidence files are pasted in the end of the email in case needed. </div><div><br></div><div>Please let me know if more info is needed. Any help is appreciated. Thank you.</div><div><br></div><div>Chia-Yi</div><div><br></div><div><br></div><div>RNA-seq evidence file:</div><div>Chr1<span class="Apple-tab-span" style="white-space:pre"> </span>assembler-aerial2_pasa<span class="Apple-tab-span" style="white-space:pre"> </span>cDNA_match<span class="Apple-tab-span" style="white-space:pre"> </span>3624<span class="Apple-tab-span" style="white-space:pre"> </span>5927<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=aerial2_align_161343;Target=asmbl_1 1082 1234 +%2Casmbl_1 692 1081 +%2Casmbl_1 572 691 +%2Casmbl_1 1 290 +%2Casmbl_1 291 571 +%2Casmbl_1 1235 1723 +</div><div>Chr1<span class="Apple-tab-span" style="white-space:pre"> </span>assembler-aerial2_pasa<span class="Apple-tab-span" style="white-space:pre"> </span>match_part<span class="Apple-tab-span" style="white-space:pre"> </span>3624<span class="Apple-tab-span" style="white-space:pre"> </span>3913<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=aerial2_align_161343-1;Parent=aerial2_align_161343</div><div>Chr1<span class="Apple-tab-span" style="white-space:pre"> </span>assembler-aerial2_pasa<span class="Apple-tab-span" style="white-space:pre"> </span>match_part<span class="Apple-tab-span" style="white-space:pre"> </span>3996<span class="Apple-tab-span" style="white-space:pre"> </span>4276<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=aerial2_align_161343-2;Parent=aerial2_align_161343</div><div><br></div><div>EST evidence file:</div><div>Chr1<span class="Apple-tab-span" style="white-space:pre"> </span>est2genome<span class="Apple-tab-span" style="white-space:pre"> </span>expressed_sequence_match<span class="Apple-tab-span" style="white-space:pre"> </span>5470<span class="Apple-tab-span" style="white-space:pre"> </span>5899<span class="Apple-tab-span" style="white-space:pre"> </span>2150<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=Chr1:hit:213:3.2.0.0;Name=gi|19829901|gb|AV795918|RAFL08-19-M04</div><div>Chr1<span class="Apple-tab-span" style="white-space:pre"> </span>est2genome<span class="Apple-tab-span" style="white-space:pre"> </span>match_part<span class="Apple-tab-span" style="white-space:pre"> </span>5470<span class="Apple-tab-span" style="white-space:pre"> </span>5899<span class="Apple-tab-span" style="white-space:pre"> </span>2150<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=Chr1:hsp:500:3.2.0.0;Parent=Chr1:hit:213:3.2.0.0;Target=gi|19829901|gb|AV795918|RAFL08-19-M04 2 431 +;Gap=M430</div><div><br></div><div>Protein evidence file:</div><div>Chr1<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>3760<span class="Apple-tab-span" style="white-space:pre"> </span>5284<span class="Apple-tab-span" style="white-space:pre"> </span>727<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=Chr1:hit:202:3.10.0.0;Name=UniRef90_M4EWW1</div><div>Chr1<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>3760<span class="Apple-tab-span" style="white-space:pre"> </span>3913<span class="Apple-tab-span" style="white-space:pre"> </span>727<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=Chr1:hsp:488:3.10.0.0;Parent=Chr1:hit:202:3.10.0.0;Target=UniRef90_M4EWW1 1 50;Gap=M31 D1 M19 F1</div><div>Chr1<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>3996<span class="Apple-tab-span" style="white-space:pre"> </span>4276<span class="Apple-tab-span" style="white-space:pre"> </span>727<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=Chr1:hsp:489:3.10.0.0;Parent=Chr1:hit:202:3.10.0.0;Target=UniRef90_M4EWW1 51 144;Gap=R1 M23 D1 M28 D1 M36 I2 M5</div></div><div><br></div></body></html>