<div dir="auto"><div>Dear Mark,<div dir="auto">Thank you for the quick reply. I'm happy to see this ignites your interest and am willing to endure your punishing questions (;</div><div dir="auto">Before I answer them, I just want to make sure we're on the same page - as far as I understand, lower AED scores indicate higher agreement with the evidence, so the "good stuff" is actually left of the 0.5 surge. Am I correct? Otherwise, this is a very poor annotation...</div><div dir="auto">Now for the questions:</div><div dir="auto">1) I did not make any filtrations so far, so single exon genes are included as well. in fact, I'm exploring the results in order to develop some criteria for filtering the genes. Would you suggest discarding single exon genes?</div><div dir="auto"><br></div><div dir="auto">2) My evidence consist of assembled transcripts, proteins and predicted gene models (pred_gff).</div><div dir="auto"><br></div><div dir="auto">3) As for repeats, I'm masking based on a repeats library obtained from a previous publication, specific to my organism of interest.</div><div dir="auto"><br></div><div dir="auto">Unfortunately, I didn't understand your final question. Could you please explain what you mean by "final build"?</div><div dir="auto"><br></div><div dir="auto">Hope these answers are helpful, and waiting to hear more thoughts.</div><div dir="auto"><br></div><div dir="auto">Thanks again.</div><br><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Apr 7, 2019, 18:11 Mark Yandell <<a href="mailto:myandell@genetics.utah.edu">myandell@genetics.utah.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal">Hi Lior,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Fun! The short answer is I don’t know. Obviously, the good stuff is on the right side of 0.5.
<span style="font-size:12.0pt"><u></u><u></u></span></p>
<p class="MsoNormal">That said, I can think of a couple of things to look into to explain the left side of the graph. Are you allowing single exon genes? Are you using RNA seq data, protein, or both? What about repeat masking? Are you doing it? Do you have
your own library? <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">My first guess, would be low complexity/repeat sequences generating more or less random blastx hits across the genome…Carson, what do you think?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">And finally, what does the AED look like for the genes included in the final build?
<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Sorry for all the questions, Lior. That’s your punishment for asking an interesting one.
<span style="font-family:"Apple Color Emoji"">😉</span><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">--mark<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">maker-devel <<a href="mailto:maker-devel-bounces@yandell-lab.org" target="_blank" rel="noreferrer">maker-devel-bounces@yandell-lab.org</a>> on behalf of Lior Glick <<a href="mailto:liorglic@mail.tau.ac.il" target="_blank" rel="noreferrer">liorglic@mail.tau.ac.il</a>><br>
<b>Date: </b>Sunday, April 7, 2019 at 7:26 AM<br>
<b>To: </b>"<a href="mailto:maker-devel@yandell-lab.org" target="_blank" rel="noreferrer">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank" rel="noreferrer">maker-devel@yandell-lab.org</a>><br>
<b>Subject: </b>[maker-devel] Curious pattern in AED distributions<u></u><u></u></span></p>
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<p class="MsoNormal">Hi MAKER users,<u></u><u></u></p>
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<p class="MsoNormal">Lately I've been performing annotations for multiple genomes from the same species.<u></u><u></u></p>
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<p class="MsoNormal">When plotting the histogram of AED scores over all genes, I repeatedly see a very specific pattern, that looks something like this:<u></u><u></u></p>
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<p class="MsoNormal"><img width="497" height="301" style="width:5.177in;height:3.1354in" id="m_-7498497327831376291_x0000_i1025" src="cid:image001.png@01D4ED21.E6C1A0E0" alt="AED_hist.png"><u></u><u></u></p>
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<p class="MsoNormal">This pattern is a bit surprising to me, in two aspects:<u></u><u></u></p>
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<p class="MsoNormal">1) Why is there a surge towards 0.5?<u></u><u></u></p>
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<p class="MsoNormal">2) Why is there a sudden drop right after that surge?<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Has anyone else seen this, or is this a specific outcome of my data/configuration?<u></u><u></u></p>
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<p class="MsoNormal">Any ideas of what may cause such a distribution?<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">While this is not necessarily an indication of a problem or bug, it does seem a bit odd, and might imply some bias or artifact.<u></u><u></u></p>
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<p class="MsoNormal">Would appreciate your comments.<u></u><u></u></p>
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<p class="MsoNormal">Thank you!<u></u><u></u></p>
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