true">1.8.</strong> Removing modification calls at the ends of reads</a></li><li class="chapter-item expanded "><a href="intro_repair.html"><strong aria-hidden="true">1.9.</strong> Repair MM/ML tags on trimmed reads</a></li><li class="chapter-item expanded "><a href="intro_motif.html"><strong aria-hidden="true">1.10.</strong> Working with sequence motifs</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="intro_motif_bed.html"><strong aria-hidden="true">1.10.1.</strong> Making a moti