om/dohlee/metheor/blob/master/img/me.png">Lee et al.</a></p>
<h2 id="calculate-entropy-in-windows-across-the-genome"><a class="header" href="#calculate-entropy-in-windows-across-the-genome">Calculate entropy in windows across the genome</a></h2>
<pre><code class="language-bash">modkit entropy --in-bam ${mod_bam} \
 -o ${output_entropy_bedgraph} \
 --ref ${ref} \
 --threads 32 \
 --log-filepath modkit_entropy.log
</code></pre>
<p>When the output file, <code>-o</code>, is omitted the output will be to stdout.