<div dir="ltr">Ah, that makes sense. Thanks!<br></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Computational Genome Science Laboratory<br>Indiana University<br>
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<br><br><div class="gmail_quote">On Thu, May 29, 2014 at 5:43 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div>There is a hidden score called abAED that measures concordance among the ab initio gene predictors . The idea was to have ab initio models that are the same across multiple ab initio predictor be kept if they're group concordance is high enough, then drop ab initio predictions that only happen in one ab initio predictor. Currently the option is all or nothing, the threshold would give a more fine grained control of keeping just some unsupported predictions.</div>
<div><br></div><div>--Carson</div><div><br></div><div><br></div><span><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> Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, May 29, 2014 at 2:47 PM<br>
<span style="font-weight:bold">To: </span> Daniel Ence <<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Cc: </span> Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span> Re: [maker-devel] Question about 'keep_pred' setting<br></div><div><div class="h5"><div><br></div><div dir="ltr">Thanks.<br><div><br>Just curious: how would the intended behavior differ if keep_pred was set to, say, 0.5, instead of 0 or 1?<br>
</div></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><br>
--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Computational Genome Science Laboratory<br>Indiana University<br></div></div><br><br><div class="gmail_quote">On Thu, May 29, 2014 at 4:44 PM, Daniel Ence <span dir="ltr"><<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">
Hi Daniel,
<div><br></div><div>Your interpretation of the code is correct. keep_preds is a binary setting. There's been some discussion behind-the-scenes about making it more flexible, but that hasn't been implemented yet. We need to fix what it says in the control file. </div>
<div><br></div><div><br></div><div><div><div><span style="font-family:Tahoma;font-size:small">Daniel Ence</span></div><div><span style="font-family:Tahoma;font-size:small">Graduate Student</span></div><div><a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a><br style="font-family:Tahoma;font-size:small">
<span style="font-family:Tahoma;font-size:small">Eccles Institute of Human Genetics</span><br style="font-family:Tahoma;font-size:small"><span style="font-family:Tahoma;font-size:small">University of Utah</span><br style="font-family:Tahoma;font-size:small">
<span style="font-family:Tahoma;font-size:small">15 North 2030 East, Room 2100</span><br style="font-family:Tahoma;font-size:small"><span style="font-family:Tahoma;font-size:small">Salt Lake City, UT 84112-5330</span></div>
</div><br><div><div>On May 29, 2014, at 2:37 PM, Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>></div><div> wrote:</div><br><blockquote type="cite"><div><div>
<div dir="ltr"><div><div>Good afternoon!<br></div><br>
I have a quick question about the keep_pred setting in Maker. In older versions of Maker, this was a binary value indicating whether unsupported predictions should be kept. I'm now using Maker 2.31.3, where it's described as a scaled value indicating a "concordance
threshold" for unsupported predictions. As far as I can tell from the code, however, it's still treated in the same way as before.<br><br></div>
Could you briefly describe the motivation for this setting and the intended (although possibly incomplete) change in its functionality in new versions of Maker?<br><br>
Thanks!<br clear="all"><div><div><div dir="ltr"><br>
--<br>
Daniel S. Standage<br>
Ph.D. Candidate<br>
Computational Genome Science Laboratory<br>
Indiana University<br></div></div></div></div></div></div>
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