<html><head><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;" class="">I would have to see the actual GFF3 files (full file including fast at the end). Give me both GFF3 files and the coordinates of the gene in question. My first guess is that you had the single_exon= filter set to different values on each run. The gene in question is an unspliced single exon gene (based on the QI), your primary piece of evidence appears to be a single exon EST, and the only value that changes in the QI is the exon overlap. Single exon evidence will be ignored by default for the AED calculation unless you have single_exon set to 1.<div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Aug 31, 2015, at 8:47 AM, Cheng, Chia-Yi <<a href="mailto:ccheng@jcvi.org" class="">ccheng@jcvi.org</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-size: 14px; font-family: Calibri, sans-serif;" class=""><div class=""><div class="">Hello MAKER team,</div><div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">Run 1: _AED=0.00;_eAED=-0.00;_QI=0|-1|0|1|-1|0|1|0|344</div><div class="">Run 2: _AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|0|344</div><div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">Please let me know if more info is needed. Any help is appreciated. Thank you.</div><div class=""><br class=""></div><div class="">Chia-Yi</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">RNA-seq evidence file:</div><div class="">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 class="">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 class="">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 class=""><br class=""></div><div class="">EST evidence file:</div><div class="">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 class="">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 class=""><br class=""></div><div class="">Protein evidence file:</div><div class="">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 class="">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 class="">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 class=""><br class=""></div></div>
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