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<div>Hi everyone,</div>
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<div>I would like to generate a list of Maker AED values comparing two datasets: a set of computationally predicted genes, and manually curated genes from the Web Apollo program. The idea is to quantify the amount of nucleotide-level change that occurred during
the manual curation process. </div>
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<div>I have tried to run Maker in several ways to generate the AED values. Both gene sets are in (as far as I can tell) valid gff3 format. First, I included the manually curated (Web Apollo) gff3 in the 'model_gff' field of maker_opts.exe, and the gff3 of the
computational predictions in the 'est_gff' field, with all of the other prediction and evidence alignment settings turned off. All resulting AEDs from this analysis were 1, even though many of the annotations had 100% overlap. Next, instead of using the computational
predictions in gff3 format, I used the fasta file of the cDNA sequence from the computational predictions in the 'est' field. Here, the results made more sense, but there was a small but significant percentage of the AED values that were 1 that actually should
have been less than 1. </div>
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<div>I have tried the 2 analyses above using both the gff3 output straight from Web Apollo, and after running the gff3 through maker once as the only entry in the model-gff field, as explained in the MAKER2 paper (http://www.biomedcentral.com/1471-2105/12/491).
This does not to appear to make a difference. </div>
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<div>Do you have any ideas where I might start to debug this?</div>
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<div>Thanks for your help!</div>
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<div>Monica</div>
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