ED of predicted open chromatin regions.</p>
<pre><code class="language-bash">$ modkit open-chromatin predict ${bam} \
  --model ${model} \
  --threshold 0.8 \
  --include-bed promoters_slop2000.bed \
  -o stdout \
  | bedtools merge -i - &gt; accessible_regions.bed
</code></pre>
<h2 id="running-with-a-gpu"><a class="header" href="#running-with-a-gpu">Running with a GPU</a></h2>
<p>Modkit comes distributed with the capability to run open chromatin prediction on a normal CPU, NVIDIA GPUs, and can be built to 