ns ${regions_bed_file} \  # BED3 or BED4 file of regions
 --cpg \  # specify CpG dinucleotides and combine strands
 --ref ${ref} \
 --threads 32 \
 --log-filepath modkit_entropy.log
</code></pre>
<p>The output must now be a directory (specified with <code>-o</code>), a bedGraph with the entropy over the windows with the regions as well as a summary of the methylation entropy in the regions will be output.
By default these files will be <code>regions.bed</code> and <code>windows.bedgraph</code>.</p>
<p>The s