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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Just a quick thought<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">The smallest summary of what you’re after might be the jaccard difference between you annotation as computed by bedtools
<a href="http://bedtools.readthedocs.org/en/latest/content/tools/jaccard.html">http://bedtools.readthedocs.org/en/latest/content/tools/jaccard.html</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">??<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> maker-devel [mailto:maker-devel-bounces@yandell-lab.org]
<b>On Behalf Of </b>Barry Moore<br>
<b>Sent:</b> Tuesday, April 19, 2016 4:37 PM<br>
<b>To:</b> Florian <fdolze@students.uni-mainz.de>; maker-devel <maker-devel@yandell-lab.org><br>
<b>Cc:</b> Campbell, Michael <mcampbel@cshl.edu><br>
<b>Subject:</b> Re: [maker-devel] A way to compare 2 annotation runs?<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The Sequence Ontology provides some tools for this:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">SOBAcl has some pre-configured reports/graphs with some flexibility to modify their content/layout.<o:p></o:p></p>
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<p class="MsoNormal"><a href="https://github.com/The-Sequence-Ontology/SOBA">https://github.com/The-Sequence-Ontology/SOBA</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">This simple example provides a table for two GFF3 files of the count of feature types:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<pre>SOBAcl --columns file --rows type --data type --data_type count \<o:p></o:p></pre>
<pre> data/dmel-all-r5.30_0001000.gff data/dmel-all-r5.30_0010000.gff <o:p></o:p></pre>
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<p class="MsoNormal">More complex examples are available in the test file SOBA/t/sobacl_test.sh<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The GAL library is a perl library that works well with MAKER output and other valid GFF3 documents. I has some scripts that would provide metrics along the lines of what you’re looking for, but is primarily a programing library to make
it easy to roll your own<o:p></o:p></p>
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<p class="MsoNormal"><a href="https://github.com/The-Sequence-Ontology/SOBA">https://github.com/The-Sequence-Ontology/GAL</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">If you’re OK with a little bit of perl code, modifying the synopsis code in the README a bit you can generate the splice complexity metrics described here (<a href="http://www.ncbi.nlm.nih.gov/pubmed/19236712">http://www.ncbi.nlm.nih.gov/pubmed/19236712</a>)
are easy to produce:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span class="pl-k"><span style="font-family:"Andale Mono",serif">use</span></span><span style="font-family:"Andale Mono",serif"> GAL::Annotation;</span><o:p></o:p></p>
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<pre><span class="pl-k"><span style="font-family:"Andale Mono",serif">my</span></span><span style="font-family:"Andale Mono",serif"> <span class="pl-smi">$annot</span> = GAL::Annotation<span class="pl-k">-></span>new(<span class="pl-pds">qw(</span><span class="pl-s">file.gff file.fasta</span><span class="pl-pds">)</span>;<o:p></o:p></span></pre>
<pre><span class="pl-k"><span style="font-family:"Andale Mono",serif">my</span></span><span style="font-family:"Andale Mono",serif"> <span class="pl-smi">$features</span> = <span class="pl-smi">$annot</span><span class="pl-k">-></span>features;<o:p></o:p></span></pre>
<pre><span style="font-family:"Andale Mono",serif"><o:p> </o:p></span></pre>
<pre><span class="pl-k"><span style="font-family:"Andale Mono",serif">my</span></span><span style="font-family:"Andale Mono",serif"> <span class="pl-smi">$genes</span> = <span class="pl-smi">$features</span><span class="pl-k">-></span>search( {<span class="pl-c1">type</span> <span class="pl-k">=></span> <span class="pl-pds">‘</span><span class="pl-s">gene</span><span class="pl-pds">'</span>} );<o:p></o:p></span></pre>
<pre><span class="pl-k"><span style="font-family:"Andale Mono",serif">while</span></span><span style="font-family:"Andale Mono",serif"> (<span class="pl-k">my</span> <span class="pl-smi">$gene</span> = <span class="pl-smi">$genes</span><span class="pl-k">-></span>next) {<o:p></o:p></span></pre>
<pre><span style="font-family:"Andale Mono",serif"> <span class="pl-c1">print</span> <span class="pl-smi">$gene</span><span class="pl-k">-></span>feature_id . <span class="pl-pds">“</span><span class="pl-cce">\t</span><span class="pl-pds">"</span>;<o:p></o:p></span></pre>
<pre><span style="font-family:"Andale Mono",serif"> print $gene->splice_complexity . “\n”;<o:p></o:p></span></pre>
<pre><span style="font-family:"Andale Mono",serif"> }<o:p></o:p></span></pre>
<pre><span style="font-family:"Andale Mono",serif">} <o:p></o:p></span></pre>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hope that helps,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Barry<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal">On Apr 19, 2016, at 9:08 AM, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I’m going to ask Michael Campbell to answer this. He wrote a protocols paper that will help.<br>
<br>
—Carson<br>
<br>
<br>
<br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On Apr 19, 2016, at 6:08 AM, Florian <<a href="mailto:fdolze@students.uni-mainz.de">fdolze@students.uni-mainz.de</a>> wrote:<br>
<br>
<br>
Hello All,<br>
<br>
We ran MAKER on a newly assembled genome for 3 iterations, since 2 seems to be the recommended standard and while on holiday I just ran it a third time. Now I want to compare the results of the iterations to see where the annotation (hopefully) improved/changed
but I cant really come up with a clever way to this.<br>
<br>
I reckon this has to be an often solved problem though I couldnt find a solution except an older entry in this mail-list but that wasnt helpful.<br>
<br>
<br>
So how are people assessing quality of a maker run? How do you say one run was 'better' than another?<br>
<br>
<br>
best regards & thanks for your input,<br>
Florian<br>
<br>
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