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<div class="">The Sequence Ontology provides some tools for this:</div>
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<div class="">SOBAcl has some pre-configured reports/graphs with some flexibility to modify their content/layout.</div>
<div class=""><a href="https://github.com/The-Sequence-Ontology/SOBA" class="">https://github.com/The-Sequence-Ontology/SOBA</a></div>
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<div class="">This simple example provides a table for two GFF3 files of the count of feature types:</div>
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<pre class="">SOBAcl --columns file --rows type --data type --data_type count \
data/dmel-all-r5.30_0001000.gff data/dmel-all-r5.30_0010000.gff </pre>
<div class="">More complex examples are available in the test file SOBA/t/sobacl_test.sh</div>
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<div class="">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</div>
<div class=""><a href="https://github.com/The-Sequence-Ontology/SOBA" class="">https://github.com/The-Sequence-Ontology/GAL</a></div>
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<div class="">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" class="">http://www.ncbi.nlm.nih.gov/pubmed/19236712</a>)
are easy to produce:</div>
<div class=""><span class="pl-k"><br class="">
</span></div>
<div class=""><font face="Andale Mono" class=""><span class="pl-k">use</span> GAL::Annotation;</font></div>
<div class="">
<pre class=""><font face="Andale Mono" class=""><span class="pl-k">my</span> <span class="pl-smi">$annot</span> = GAL::Annotation<span class="pl-k">-></span>new(<span class="pl-s"><span class="pl-pds">qw(</span>file.gff file.fasta<span class="pl-pds">)</span></span>;
<span class="pl-k">my</span> <span class="pl-smi">$features</span> = <span class="pl-smi">$annot</span><span class="pl-k">-></span>features;
<span class="pl-k">my</span> <span class="pl-smi">$genes</span> = <span class="pl-smi">$features</span><span class="pl-k">-></span>search( {<span class="pl-c1">type</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">‘</span>gene<span class="pl-pds">'</span></span>} );
<span class="pl-k">while</span> (<span class="pl-k">my</span> <span class="pl-smi">$gene</span> = <span class="pl-smi">$genes</span><span class="pl-k">-></span>next) {
<span class="pl-c1">print</span> <span class="pl-smi">$gene</span><span class="pl-k">-></span>feature_id . <span class="pl-s"><span class="pl-pds">“</span><span class="pl-cce">\t</span><span class="pl-pds">"</span></span>;
print $gene->splice_complexity . “\n”;
}
}
</font></pre>
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<div class="">Hope that helps,</div>
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<div class="">Barry</div>
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<blockquote type="cite" class="">
<div class="">On Apr 19, 2016, at 9:08 AM, Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">I’m going to ask Michael Campbell to answer this. He wrote a protocols paper that will help.<br class="">
<br class="">
—Carson<br class="">
<br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">On Apr 19, 2016, at 6:08 AM, Florian <<a href="mailto:fdolze@students.uni-mainz.de" class="">fdolze@students.uni-mainz.de</a>> wrote:<br class="">
<br class="">
<br class="">
Hello All,<br class="">
<br class="">
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 class="">
<br class="">
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 class="">
<br class="">
<br class="">
So how are people assessing quality of a maker run? How do you say one run was 'better' than another?<br class="">
<br class="">
<br class="">
best regards & thanks for your input,<br class="">
Florian<br class="">
<br class="">
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</blockquote>
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