<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Yes. maker2zff tries to further select a subset of the best supported models by requiring multiple forms of evidence support.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 7, 2019, at 10:42 PM, Xabier Vázquez-Campos <<a href="mailto:xvazquezc@gmail.com" class="">xvazquezc@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">If you train SNAP, the maker2zff script has internal quality cutoffs based on the existence of evidence. e.g. by default it will require having some EST evidence<br class=""></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 8 Apr 2019 at 11:32, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">That’s interesting. It could be a handful of internal filters that help with spurious results.<br class="">
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I use a 0.5 sensitivity/specificity to identify shared edges for a jaccardian split on overlapping evidence clusters for example. There are also a couple of places where if the only thing supporting a model is a single exon blastx hit (i.e. no exonerate, ab initio model, or est splice support, but just a chunk od single exon blastx) then maker will use a reading frame aware AED value of 0.5 as a filter (as in it checks if the reading frame matches and not just raw overlap). If that’s the case, the spike near 0.5 may indicate I needed to be a little strickter than my empirical cutoff estimate. Perhaps 0.4 or 0.45 would be the better cuttoff for these spurious blastx induced models.<br class="">
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—Carson<br class="">
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<br class="">
> On Apr 7, 2019, at 7:25 AM, Lior Glick <<a href="mailto:liorglic@mail.tau.ac.il" target="_blank" class="">liorglic@mail.tau.ac.il</a>> wrote:<br class="">
> <br class="">
> Hi MAKER users,<br class="">
> Lately I've been performing annotations for multiple genomes from the same species.<br class="">
> When plotting the histogram of AED scores over all genes, I repeatedly see a very specific pattern, that looks something like this:<br class="">
> <AED_hist.png><br class="">
> This pattern is a bit surprising to me, in two aspects:<br class="">
> 1) Why is there a surge towards 0.5?<br class="">
> 2) Why is there a sudden drop right after that surge?<br class="">
> <br class="">
> Has anyone else seen this, or is this a specific outcome of my data/configuration?<br class="">
> Any ideas of what may cause such a distribution?<br class="">
> <br class="">
> 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.<br class="">
> Would appreciate your comments.<br class="">
> Thank you!<br class="">
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</blockquote></div><br clear="all" class=""><br class="">-- <br class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">Xabier Vázquez-Campos, <i class="">PhD</i><br class=""><i class="">Research Associate</i><br class="">NSW Systems Biology Initiative<br class="">School of Biotechnology and Biomolecular Sciences<br class="">
The University of New South Wales<br class="">Sydney NSW 2052 AUSTRALIA<br class=""></div></div></div></div></div></div></div></div></div></div></div>
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