>duplex</a> reads). For CpGs in the example above the
<code>MM</code> tags would be <code>C+m?</code> and <code>G-m?</code> for the top-strand and bottom-strand cytosines, respectively.</p>
<p>The <code>modkit pileup-hemi</code> command will perform an aggregation of the methylation "patterns" at genomic positions. An example
command to perform hemi-methylation analysis at CpGs would be</p>
<pre><code class="language-bash">modkit pileup-hemi \
  /path/to/duplex_reads.bam \
  --cpg \
  -r /path/to/reference.