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<ol class="chapter"><li class="chapter-item expanded "><a href="quick_start.html"><strong aria-hidden="true">1.</strong> Quick Start guides</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="intro_bedmethyl.html"><strong aria-hidden="true">1.1.</strong> Constructing bedMethyl tables</a></li><li class="chapter-item expanded "><a href="intro_pileup_hemi.html"><strong aria-hidden="true">1.2.</strong> Make hemi-methylation bedMethyl tables</a></li><li class="chapter-item expanded "><a href="intro_adjust.html"><strong aria-hidden="true">1.3.</strong> Updating and adjusting MM tags</a></li><li class="chapter-item expanded "><a href="intro_sample_probs.html"><strong aria-hidden="true">1.4.</strong> Inspecting base modification probabilities</a></li><li class="chapter-item expanded "><a href="intro_summary.html"><strong aria-hidden="true">1.5.</strong> Summarizing a modBAM</a></li><li class="chapter-item expanded "><a href="intro_stats.html"><strong aria-hidden="true">1.6.</strong> Calculating modification statistics in regions</a></li><li class="chapter-item expanded "><a href="intro_call_mods.html"><strong aria-hidden="true">1.7.</strong> Calling mods in a modBAM</a></li><li class="chapter-item expanded "><a href="intro_edge_filter.html"><strong aria-hidden="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 motif BED file</a></li><li class="chapter-item expanded "><a href="intro_find_motifs.html"><strong aria-hidden="true">1.10.2.</strong> Find highly modified motif sequences</a></li><li class="chapter-item expanded "><a href="evaluate_motif.html" class="active"><strong aria-hidden="true">1.10.3.</strong> Evaluate and refine a table of known motifs</a></li></ol></li><li class="chapter-item expanded "><a href="intro_extract.html"><strong aria-hidden="true">1.11.</strong> Extracting read information to a table</a></li><li class="chapter-item expanded "><a href="intro_localize.html"><strong aria-hidden="true">1.12.</strong> Investigating patterns with localise</a></li><li class="chapter-item expanded "><a href="intro_dmr.html"><strong aria-hidden="true">1.13.</strong> Perform differential methylation scoring</a></li><li class="chapter-item expanded "><a href="intro_validate.html"><strong aria-hidden="true">1.14.</strong> Validate ground truth results</a></li><li class="chapter-item expanded "><a href="intro_entropy.html"><strong aria-hidden="true">1.15.</strong> Calculating methylation entropy</a></li><li class="chapter-item expanded "><a href="intro_include_bed.html"><strong aria-hidden="true">1.16.</strong> Narrow output to specific positions</a></li></ol></li><li class="chapter-item expanded "><a href="advanced_usage.html"><strong aria-hidden="true">2.</strong> Extended subcommand help</a></li><li class="chapter-item expanded "><a href="troubleshooting.html"><strong aria-hidden="true">3.</strong> Troubleshooting</a></li><li class="chapter-item expanded "><a href="faq.html"><strong aria-hidden="true">4.</strong> Frequently asked questions</a></li><li class="chapter-item expanded "><a href="limitations.html"><strong aria-hidden="true">5.</strong> Current limitations</a></li><li class="chapter-item expanded "><a href="perf_considerations.html"><strong aria-hidden="true">6.</strong> Performance considerations</a></li><li class="chapter-item expanded "><a href="algo_details.html"><strong aria-hidden="true">7.</strong> Algorithm details</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="filtering.html"><strong aria-hidden="true">7.1.</strong> Pass/fail base modification calls</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="filtering_details.html"><strong aria-hidden="true">7.1.1.</strong> Threshold examples</a></li><li class="chapter-item expanded "><a href="filtering_numeric_details.html"><strong aria-hidden="true">7.1.2.</strong> Numeric details</a></li></ol></li><li class="chapter-item expanded "><a href="dmr_scoring_details.html"><strong aria-hidden="true">7.2.</strong> DMR model and scoring details</a></li><li class="chapter-item expanded "><a href="collapse.html"><strong aria-hidden="true">7.3.</strong> Ignoring and combining calls</a></li></ol></li></ol>
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<h1 id="evaluate-a-table-of-known-motifs"><a class="header" href="#evaluate-a-table-of-known-motifs">Evaluate a table of known motifs</a></h1>
<p>The <code>modkit search</code> command has an option to provide any number of known motifs with <code>--know-motif</code>.
If you already have a list of candidate motifs (e.f. from a previous run of <code>modkit motif search</code>) you can check these motifs quickly against a bedMethyl table with <code>modkit motif evaluate</code>.</p>
<pre><code class="language-bash">modkit motif evaluate -i ${bedmethyl} --known-motifs-table motifs.tsv -r ${ref}
</code></pre>
<p>Similarly, the search <a href="./intro_find_motifs.html#simple-description-of-the-search-algorithm">algorithm</a> can be run using known motifs as seeds:</p>
<pre><code class="language-bash">modkit motif refine -i ${bedmethyl} --known-motifs-table motifs.tsv -r ${ref}
</code></pre>
<p>The output tables to both of these commands have the same schema:</p>
<div class="table-wrapper"><table><thead><tr><th>column</th><th>name</th><th>description</th><th>type</th></tr></thead><tbody>
<tr><td>1</td><td>mod_code</td><td>code specifying the modification found in the motif</td><td>str</td></tr>
<tr><td>2</td><td>motif</td><td>sequence of identified motif using <a href="https://www.bioinformatics.org/sms/iupac.html">IUPAC</a> codes</td><td>str</td></tr>
<tr><td>3</td><td>offset</td><td>0-based offset into the motif sequence of the modified base</td><td>int</td></tr>
<tr><td>4</td><td>frac_mod</td><td>fraction of time this sequence is found in the <em>high modified</em> set col-5 / (col-5 + col-6)</td><td>float</td></tr>
<tr><td>5</td><td>high_count</td><td>number of occurances of this sequence in the <em>high-modified</em> set</td><td>int</td></tr>
<tr><td>6</td><td>low_count</td><td>number of occurances of this sequence in the <em>low-modified</em> set</td><td>int</td></tr>
<tr><td>7</td><td>mid_count</td><td>number of occurances of this sequence in the <em>mid-modified</em> set</td><td>int</td></tr>
<tr><td>8</td><td>log_odds</td><td>log2 odds of the motif being in the high-modified set</td><td>int</td></tr>
</tbody></table>
</div>
<p>In the human-readable table columns (1) and (2) are merged to show the modification code in the motif sequence context, the rest of the columns are the same as the machine-readable table.</p>

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