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<div>
<span class="notice">Filtering is performed using BBTools rqcfilter.sh script.</span> <br />
</div>
<div style="padding: 10px">
<h2 class="section-title"> Fastq Files </h2>
<div class="section">
<table class='data'>
<tr>
<th></th>
<th>Number of Reads </th>
<th>File Size</th>
<th>File Location</th>
</tr>
<tr>
<th>Input FASTQ</th>
<td>[_RAW-READ-CNT_]</td>
<td>[_RAW-FILE-SIZE_] MB</td>
<td>[_RAW-FILE-LOCATION_]</td>
</tr>
<tr>
<th>Filtered FASTQ</th>
<td>[_FILTERED-READ-CNT_]</td>
<td>[_FILTERED-FILE-SIZE_] MB</td>
<td>[_FILTERED-FILE-LOCATION_]</td>
</tr>
<tr>
<th>Filtered %</th>
<td>[_REMOVED-READ-PCT_]%</td>
<td>-</td>
<td>-</td>
</tr>
</table>
<span class="notice">The file size for the filtered fastq is significantly smaller than the input fastq because the reads were re-ordered to optimize gzip file compression.</span>
</div>
<br />
<h2 class="section-title"> Filtering Metrics </h2>
<div class="section">
<table class='hori, border, data'>
<tr>
<th>Metric</th>
<th>Read Count</th>
<th>Base Count</th>
</tr>
<tr>
<th>Input</th>
<td>[_RAW-READ-CNT_]</td>
<td>[_RAW-BASE-CNT_]</td>
</tr>
<tr>
<th>Remaining</th>
<td>[_FILTERED-READ-CNT_]</td>
<td>[_FILTERED-BASE-CNT_]</td>
</tr>
<tr>
<th>Percentage Removed</th>
<td>[_REMOVED-READ-PCT_]%</td>
<td>[_REMOVED-BASE-PCT_]%</td>
</tr>
</table>
</div>
<br />
<div class="section">
<table class='data'>
<tr>
<th>Metric</th>
<th>Percent </th>
<th>Read Count</th>
</tr>
<tr>
<th>Low Quality Removed</th>
<td>[_LOW-QUAL-REMOVED-PCT_]</td>
<td>[_LOW-QUAL-REMOVED-READ-CNT_]</td>
</tr>
<tr>
<th>Artifact Removed</th>
<td>[_ARTI-REMOVED-PCT_]</td>
<td>[_ARTI-REMOVED-READ-CNT_]</td>
</tr>
<tr>
<th>Ribosomal RNA Removed</th>
<td>[_RRNA-REMOVED-READ-PCT_]</td>
<td>[_RRNA-REMOVED-READ-CNT_]</td>
</tr>
<tr>
<th>Microbial Removed</th>
<td>[_MICROBE-REMOVED-READ-PCT_]</td>
<td>[_MICROBE-REMOVED-READ-CNT_]</td>
</tr>
<tr>
<th>Human Filtered</th>
<td>[_HUMAN-REMOVED-READ-PCT_]</td>
<td>[_HUMAN-REMOVED-READ-CNT_]</td>
</tr>
<tr>
<th>Dog Filtered</th>
<td>[_DOG-REMOVED-READ-PCT_]</td>
<td>[_DOG-REMOVED-READ-CNT_]</td>
</tr>
<tr>
<th>Cat Filtered</th>
<td>[_CAT-REMOVED-READ-PCT_]</td>
<td>[_CAT-REMOVED-READ-CNT_]</td>
</tr>
<tr>
<th>Mouse Filtered</th>
<td>[_MOUSE-REMOVED-READ-PCT_]</td>
<td>[_MOUSE-REMOVED-READ-CNT_]</td>
</tr>
</table>
<!-- ul>
<li>Filter log: [_FILTER-LOG_] ([_FILTER-LOG-SIZE_] KB)</li>
<li>Filter Text Report: [_FILTER-REPORT_] ([_FILTER-REPORT-SIZE_] KB) filter.txt (878.0 bytes)</li>
</ul -->
</div>
<br />
[_FILTERED-READ-QC_]
</div>
|
