<div dir="ltr">One more point. The sensitivity, specificity,and accuracy produced by the <a href="http://compare_annotations_3.2.pl/" target="_blank" style="font-family:arial,sans-serif;font-size:12.666666984558105px">compare_annotations_3.2.pl</a><font face="arial, sans-serif"><span style="font-size:12.666666984558105px"> script are gene level, and overlap is defined very liberally between annotation sets is defined as at least one nucleotide of an exon overlap.</span></font><div>
<font face="arial, sans-serif"><span style="font-size:12.666666984558105px">Mike</span></font></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Mar 10, 2014 at 9:47 AM, Michael Campbell <span dir="ltr"><<a href="mailto:michael.s.campbell1@gmail.com" target="_blank">michael.s.campbell1@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 dir="ltr">Hi Robert,<div><br></div><div>Here are the scripts that were mentioned before.</div><div><br></div><div>
The AED_cdf_generator.pl script is for making cumulative distribution function plots based on annotation edit distance. This script is quite simple and strait forward in its internals.</div>
<div><br></div><div>The <a href="http://compare_annotations_3.2.pl" target="_blank">compare_annotations_3.2.pl</a> script is for generating summary stats for annotations and will compare two annotations of the same assembly. </div>
<div><br>
</div><div>You can run either script without arguments to get a usage statement.</div><div><br></div><div>Thanks,</div><div>Mike</div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div class="h5">On Mon, Mar 10, 2014 at 6:17 AM, Robert King (RRes-Roth) <span dir="ltr"><<a href="mailto:robert.king@rothamsted.ac.uk" target="_blank">robert.king@rothamsted.ac.uk</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
<div lang="EN-GB" link="blue" vlink="purple">
<div>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white">Dear Maker Developers,<span> <u></u><u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white"><u></u> <u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white">I’ve updated a reference that was had errors and was a little incomplete and now trying to produce a annotation
for it. Please note the reference has not changed dramatically. I’ve produced two annotations using as evidence:<u></u><u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white"><u></u> <u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white">Annotation 1:<u></u><u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white">Uniprot proteins search using species keyword “fusarium”<u></u><u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white">Pubmed mRNA for the name of the organism
<u></u><u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white">Prior annotation reference transcripts<u></u><u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white"><u></u> <u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white">Annotation 2:<u></u><u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white">Uniprot proteins search using species keyword “fusarium”<u></u><u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white">Pubmed mRNA for the name of the organism
<u></u><u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white">Prior annotation reference transcripts<u></u><u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white">mRNA trinity assembly pasafly of different strain (only RNA-seq available)<u></u><u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white"><u></u> <u></u></span></span></p>
<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;background:white">I’m not sure if it was a smart move to use the prior annotation reference transcripts?</span></span><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I want to compare these two annotations and have produced AED scores. How do I generate summary stats/figures to compare annotations. You mentioned last year in a post Mike Campbell has a script to produce these, do you know if he will
post it? I’ve got the Eval program and converted to gtf format using the provided script, just waiting on some perl modules to be installed by admin to test it. I’m waiting on some perl modules to be installed by our administrator to test out the “Evaluator”
and “compare” programs too, what do they do?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Best Wishes<u></u><u></u></p>
<p class="MsoNormal">Rob<span><font color="#888888"><u></u><u></u></font></span></p><span><font color="#888888">
</font></span></div><span><font color="#888888">
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<br></div></blockquote></div><span class="HOEnZb"><font color="#888888"><br><br clear="all"><div><br></div>-- <br><div dir="ltr">Michael Campbell MS, RD.<br>Doctoral Candidate<br>Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330<br>ph:585-3543<br><br></div>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">Michael Campbell MS, RD.<br>Doctoral Candidate<br>Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330<br>ph:585-3543<br><br></div>
</div>