<html><head></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>No. It should use whichever is lower the AED or eAED score. The only exception is model_gff results. Those are always kept. Also note that the filter is for the entire gene, not just individual splice forms if you have alternate splicing.</div><div><br></div><div>If you want I can take a look if there is anything non-obvious. You would have to send me the final GFF3 and the maker_opts.ctl file.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Jan Philip Øyen <<a href="mailto:janphilipoyen@gmail.com">janphilipoyen@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, June 3, 2014 at 9:07 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] AED scores and thresholds: Not filtering?<br></div><div><br></div><div dir="ltr">Hello,<br>We are currently working on annotating arthropod genomes with the maker pipeline. We have tried to filter out genes with low support using the AED thresholds using AED_threshold=0.5. However, we still find genes without scores and most importantly genes with scores above the set threshold (even AED=1). Is there a known issue which could cause this? <br><br>We can supply the control files as well as gffs, but would not like to make them public at this stage. <br><br>Best Regards,<br>Jan Philip Oeyen<br>ZFMK / ZMB / University of Bonn<br></div>
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