[maker-devel] AED scores from MAKER pipeline - deterministic or not?

[Cheng, Chia-Yi]

Hello MAKER team,

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.

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:

Run 1: _AED=0.00;_eAED=-0.00;_QI=0|-1|0|1|-1|0|1|0|344
Run 2: _AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|0|1|0|344

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.

Please let me know if more info is needed. Any help is appreciated. Thank you.

Chia-Yi


RNA-seq evidence file:
Chr1 assembler-aerial2_pasa cDNA_match 3624 5927 . + . 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 +
Chr1 assembler-aerial2_pasa match_part 3624 3913 . + . ID=aerial2_align_161343-1;Parent=aerial2_align_161343
Chr1 assembler-aerial2_pasa match_part 3996 4276 . + . ID=aerial2_align_161343-2;Parent=aerial2_align_161343

EST evidence file:
Chr1 est2genome expressed_sequence_match 5470 5899 2150 - . ID=Chr1:hit:213:3.2.0.0;Name=gi|19829901|gb|AV795918|RAFL08-19-M04
Chr1 est2genome match_part 5470 5899 2150 - . 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

Protein evidence file:
Chr1 protein2genome protein_match 3760 5284 727 + . ID=Chr1:hit:202:3.10.0.0;Name=UniRef90_M4EWW1
Chr1 protein2genome match_part 3760 3913 727 + . 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
Chr1 protein2genome match_part 3996 4276 727 + . 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

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