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<div>Thank you for the prompt reply, Carson! Yes, my gff3 was modeled as gene models, not match/match_part, so reformatting it may do the trick.</div>
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<div>Monica</div>
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<span style="font-weight:bold">From: </span>Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Friday, November 7, 2014 at 10:26 AM<br>
<span style="font-weight:bold">To: </span>Monica Poelchau <<a href="mailto:monica.poelchau@ars.usda.gov">monica.poelchau@ars.usda.gov</a>><br>
<span style="font-weight:bold">Cc: </span>"<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [maker-devel] calculating AED values between two datasets<br>
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If you got every value as 1 with the est_gff, then your GFF3 didn’t load. The est_gff option is expecting match/match_part format alignment format, and you may not have had it correctly structures.
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<div class="">For using fasta files instead, you may also need to set single_exon=1 and single_length=1, otherwise many of those alignments will be ignored for AED scoring purposes. You should also look out the output in a viewer like apollo to visualize the
comparison to see if the reason you get 1 is because the aligner can’t recover the original transcript alignment.
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<div class="">—Carson</div>
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<div class="">On Nov 7, 2014, at 6:17 AM, Poelchau, Monica <<a href="mailto:monica.poelchau@ars.usda.gov" class="">monica.poelchau@ars.usda.gov</a>> wrote:</div>
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<div class="">Hi everyone,</div>
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<div class="">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 class="">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 class="">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 (<a href="http://www.biomedcentral.com/1471-2105/12/491" class="">http://www.biomedcentral.com/1471-2105/12/491</a>).
This does not to appear to make a difference. </div>
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<div class="">Do you have any ideas where I might start to debug this?</div>
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<div class="">Thanks for your help!</div>
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<div class="">Monica</div>
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