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report.xsl
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<?xml version="1.0"?>
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<xsl:output method="html" doctype-system="http://www.w3.org/TR/html4/strict.dtd" doctype-public="-//W3C//DTD HTML 4.01//EN" indent="yes" />
<xsl:template name="RepeatString">
<xsl:param name="string" select="''" />
<xsl:param name="times" select="1" />
<xsl:if test="number($times) > 0">
<xsl:value-of select="$string" />
<xsl:call-template name="RepeatString">
<xsl:with-param name="string" select="$string" />
<xsl:with-param name="times" select="$times - 1" />
</xsl:call-template>
</xsl:if>
</xsl:template>
<xsl:template name="format-suffix">
<xsl:param name="myval" />
<xsl:param name="precision" />
<xsl:variable name="zeroes">
<xsl:call-template name="RepeatString">
<xsl:with-param name="string" select="0" />
<xsl:with-param name="times" select="$precision" />
</xsl:call-template>
</xsl:variable>
<xsl:variable name="dval" select="concat(1,$zeroes)" />
<xsl:choose>
<xsl:when test="$myval > 1000000000">
<xsl:value-of select="format-number(round($myval div (1000000000 div $dval)) div $dval, concat('#.',$zeroes))" />
<xsl:text>G</xsl:text>
</xsl:when>
<xsl:when test="$myval > 1000000">
<xsl:value-of select="format-number(round($myval div (1000000 div $dval)) div $dval, concat('#.',$zeroes))" />
<xsl:text>M</xsl:text>
</xsl:when>
<xsl:when test="$myval > 1000">
<xsl:value-of select="format-number(round($myval div (1000 div $dval)) div $dval, concat('#.',$zeroes))" />
<xsl:text>k</xsl:text>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="$myval" />
</xsl:otherwise>
</xsl:choose>
</xsl:template>
<xsl:template match="/SequencingReport">
<html>
<head>
<title> <xsl:value-of select="MetaData/@Project"/> - <xsl:value-of select="MetaData/@RunFolder"/></title>
<style type="text/css">
body {font:12px arial,sans-serif; background:#ffffff}
h1 {text-align: left; padding: 5px; font-weight:bold; font-size:150%;}
h2 {text-align: left; padding: 5px; font-weight:bold; font-size:120%;}
hr {color:sienna;}
p {margin-left:20px; width: 80em;}
tr.even { background: #bbbbbb; }
tr.odd { background: #dddddd; }
thead { background: #eeeeee; }
div.section {display: inline-block; background: #eeeeee; margin-bottom: 20px; margin-right: 20px;}
table th { padding: 1px 10px;}
table td { padding: 1px 10px;}
table td { text-align: center;}
table td.SampleName { text-align: left; padding: 5px; font-weight:bold; font-size:100%;}
span.stddev {font-size:75%;}
table.MetaData th { text-align: left; padding: 5px; font-weight:bold; font-size:100%;}
table.MetaData td { text-align: left; padding: 5px; font-size:75%; background:#dddddd}
table.key th { text-align: left; padding: 5px; font-size:75%;}
table.key td { text-align: left; padding: 5px; font-size:75%; background:#dddddd}
</style>
</head>
<body>
<h1>Sequencing results for <xsl:value-of select="MetaData/@Project"/>
in run <xsl:value-of select="MetaData/@RunFolder"/></h1>
<br />
<div>
<div class="section">
<h2>Metrics aggregated per lane</h2>
<table>
<thead>
<tr>
<th>Lane</th>
<th>Raw Density<br/>clusters/mm<sup>2</sup></th>
<th>Pass<br/>Filter(%)</th>
<th>Clusters<br/>PF</th>
<th>Read</th>
<th>Yield<br/>PF (bp)</th>
<th>Q≥30(%)</th>
<th>Yield<br/>Q≥30 (bp)</th>
<th>MeanQ</th>
<th>PhiX<br/>Error</th>
<th>Q-score per base A/C/G/T</th>
<th>Q-score<br/>distribution</th>
<th>Base<br/>composition</th>
<th>GC<br/>distribution</th>
<th>Contiguous Length<br/>with Q≥30 (bp)</th>
<th>Duplicates</th>
<th>Adapter<br/>sequences</th>
<th>Q-score per base<br/>and position</th>
</tr>
</thead>
<tbody>
<xsl:for-each select="LaneMetrics/Lane">
<xsl:variable name="row-class">
<xsl:choose>
<xsl:when test="position() mod 2 = 0">even</xsl:when>
<xsl:otherwise>odd</xsl:otherwise>
</xsl:choose>
</xsl:variable>
<xsl:variable name="LaneRows">
<xsl:value-of select="count(descendant::Read)"/>
</xsl:variable>
<xsl:for-each select="./Read">
<tr class="{$row-class}">
<xsl:if test="count(preceding-sibling::Read) = 0">
<td rowspan="{$LaneRows}"><xsl:value-of select="../@Id"/></td>
<td rowspan="{$LaneRows}">
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@DensityRaw" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
<td rowspan="{$LaneRows}"><xsl:value-of select="@PctPF"/></td>
<td rowspan="{$LaneRows}">
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@PF" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
</xsl:if>
<td><xsl:value-of select="@Id"/></td>
<td>
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@YieldPF" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
<td><xsl:value-of select="format-number(round((@YieldQ30 * 1000) div @YieldPF) div 10, '##.0')"/></td>
<td>
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@YieldQ30" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
<td><xsl:value-of select="@QMean"/><span class="stddev">±<xsl:value-of select="@QStdDev"/></span></td>
<td><xsl:value-of select="@ErrRate"/><span class="stddev">±<xsl:value-of select="@ErrRateSD"/></span></td>
<td>
<xsl:value-of select="@QValuePerBaseAMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseAStdv"/></span><br/>
<xsl:value-of select="@QValuePerBaseCMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseCStdv"/></span><br/>
<xsl:value-of select="@QValuePerBaseGMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseGStdv"/></span><br/>
<xsl:value-of select="@QValuePerBaseTMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseTStdv"/></span>
</td>
<xsl:choose>
<xsl:when test="@QscorePlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@QscorePlot)}"><img alt="Qscore Plot" src="{concat('./',@QscorePlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@BaseCompPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@BaseCompPlot)}"><img alt="Base Composition Plot" src="{concat('./',@BaseCompPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@GCPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@GCPlot)}"><img alt="GC Plot" src="{concat('./',@GCPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@Q30Plot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@Q30Plot)}"><img alt="Q30Length Plot" src="{concat('./',@Q30PlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@DupPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@DupPlot)}"><img alt="Duplication Plot" src="{concat('./',@DupPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@AdapterPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@AdapterPlot)}"><img alt="Adapter Plot" src="{concat('./',@AdapterPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@QValuePerBase = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@QValuePerBase)}"><img alt="Q-value per base" src="{concat('./',@QValuePerBaseThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
</tr>
</xsl:for-each>
</xsl:for-each>
</tbody>
</table>
</div>
</div>
<div>
<div class="section">
<h2>Metrics per sample</h2>
<table>
<thead>
<tr>
<th>Lane</th>
<th>Tag</th>
<xsl:if test="not(@SampleNumber='')">
<th>Sample Number</th>
</xsl:if>
<th>Library</th>
<th>Insert<br/>size(bp)</th>
<th>Fraction<br/>of lane(%)</th>
<th>Clusters<br/>PF</th>
<th>Tags with<br/>error(%)</th>
<th>Read</th>
<th>Yield<br/>PF (bp)</th>
<th>Q≥30(%)</th>
<th>Yield<br/>Q≥30 (bp)</th>
<th>MeanQ</th>
<th>Q-score per base A/C/G/T</th>
<th>Q-score<br/>distribution</th>
<th>Base<br/>composition</th>
<th>GC<br/>distribution</th>
<th>Contiguous Length<br/>with Q≥30 (bp)</th>
<th>Duplicates</th>
<th>Adapter<br/>sequences</th>
<th>Q-score per base<br/> and position</th>
</tr>
</thead>
<tbody>
<xsl:for-each select="SampleMetrics/Sample">
<xsl:variable name="row-class">
<xsl:choose>
<xsl:when test="position() mod 2 = 0">even</xsl:when>
<xsl:otherwise>odd</xsl:otherwise>
</xsl:choose>
</xsl:variable>
<tr class="{$row-class}">
<xsl:if test="not(@SampleNumber='')">
<td colspan="21" class="SampleName"><xsl:value-of select="@Id"/></td>
</xsl:if>
<xsl:if test="@SampleNumber=''">
<td colspan="20" class="SampleName"><xsl:value-of select="@Id"/></td>
</xsl:if>
</tr>
<xsl:for-each select="./Tag">
<xsl:for-each select="./Lane">
<xsl:variable name="LaneRows">
<xsl:value-of select="count(descendant::Read)"/>
</xsl:variable>
<xsl:for-each select="./Read">
<tr class="{$row-class}">
<xsl:if test="count(preceding-sibling::Read) = 0">
<td rowspan="{$LaneRows}"><xsl:value-of select="../@Id"/></td>
<td rowspan="{$LaneRows}"><xsl:value-of select="../../@Id"/></td>
<xsl:if test="not(@SampleNumber='')">
<td rowspan="{$LaneRows}"><xsl:value-of select="@SampleNumber"/></td>
</xsl:if>
<td rowspan="{$LaneRows}"><xsl:value-of select="@LibraryName"/></td>
<td rowspan="{$LaneRows}">
<xsl:if test="not(@FragmentLower='') and not(@FragmentUpper='')">
<xsl:value-of select="concat(@FragmentSize,' (',@FragmentLower, '-', @FragmentUpper, ')')"/>
</xsl:if>
<xsl:if test="@FragmentLower='' or @FragmentUpper=''">
<xsl:value-of select="@FragmentSize"/>
</xsl:if>
</td>
<td rowspan="{$LaneRows}"><xsl:value-of select="round(100*@PctLane) div 100"/></td>
<td rowspan="{$LaneRows}">
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@PF" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
<td rowspan="{$LaneRows}"><xsl:value-of select="format-number(round(100*@TagErr) div 100,'##.0')"/></td>
</xsl:if>
<td><xsl:value-of select="@Id"/></td>
<td>
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@YieldPF" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
<!-- <td><xsl:value-of select="@Q30Fraction"/></td> -->
<td><xsl:value-of select="format-number(round((@YieldQ30 * 1000) div @YieldPF) div 10, '##.0')"/></td>
<td>
<xsl:call-template name="format-suffix">
<xsl:with-param name="myval" select="@YieldQ30" />
<xsl:with-param name="precision" select="1" />
</xsl:call-template>
</td>
<td><xsl:value-of select="@QMean"/><span class="stddev">±<xsl:value-of select="@QStdDev"/></span></td>
<td>
<xsl:value-of select="@QValuePerBaseAMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseAStdv"/></span><br/>
<xsl:value-of select="@QValuePerBaseCMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseCStdv"/></span><br/>
<xsl:value-of select="@QValuePerBaseGMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseGStdv"/></span><br/>
<xsl:value-of select="@QValuePerBaseTMean"/><span class="stddev">±<xsl:value-of select="@QValuePerBaseTStdv"/></span>
</td>
<xsl:choose>
<xsl:when test="@QscorePlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@QscorePlot)}"><img alt="Qscore Plot" src="{concat('./',@QscorePlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@BaseCompPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@BaseCompPlot)}"><img alt="Base Composition Plot" src="{concat('./',@BaseCompPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@GCPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@GCPlot)}"><img alt="GC Plot" src="{concat('./',@GCPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@Q30Plot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@Q30Plot)}"><img alt="Q30Length Plot" src="{concat('./',@Q30PlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@DupPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@DupPlot)}"><img alt="Duplication Plot" src="{concat('./',@DupPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@AdapterPlot = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@AdapterPlot)}"><img alt="Adapter Plot" src="{concat('./',@AdapterPlotThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
<xsl:choose>
<xsl:when test="@QValuePerBase = 'NA'">
<td>NA</td>
</xsl:when>
<xsl:otherwise>
<td><a href="{concat('./',@QValuePerBase)}"><img alt="Q-value per base" src="{concat('./',@QValuePerBaseThumb)}"/></a></td>
</xsl:otherwise>
</xsl:choose>
</tr>
</xsl:for-each>
</xsl:for-each>
</xsl:for-each>
</xsl:for-each>
</tbody>
</table>
</div>
</div>
<div>
<div class="section">
<h2>Run parameters</h2>
<table class="MetaData">
<tr class="odd">
<td>Run Folder</td>
<td><xsl:value-of select="MetaData/@RunFolder"/></td>
</tr>
<xsl:for-each select="MetaData/Read">
<tr >
<td>Read <xsl:value-of select="@Id"/></td>
<td><xsl:value-of select="@Cycles"/>bp</td>
</tr>
</xsl:for-each>
<tr >
<td>Cluster Kit</td>
<td><xsl:value-of select="MetaData/@ClusterKitVersion"/></td>
</tr>
<tr >
<td>Flow Cell ID</td>
<td><xsl:value-of select="MetaData/@FlowCellId"/></td>
</tr>
<tr >
<td>Flow Cell Version</td>
<td><xsl:value-of select="MetaData/@FlowCellVer"/></td>
</tr>
<tr >
<td>Chemistry</td>
<td><xsl:value-of select="MetaData/@SBSversion"/></td>
</tr>
<tr >
<td>Instrument Type</td>
<td><xsl:value-of select="MetaData/@InstrumentModel"/></td>
</tr>
<tr >
<td>Instrument Control Software</td>
<td><xsl:value-of select="MetaData/@CsVersion"/></td>
</tr>
<tr >
<td>RTA Version</td>
<td><xsl:value-of select="MetaData/@RtaVersion"/></td>
</tr>
<tr >
<td>Sisyphus Version</td>
<td><xsl:value-of select="MetaData/@SisyphusVersion"/></td>
</tr>
<tr >
<td>Q-Score Offset</td>
<td><xsl:value-of select="MetaData/@Qoffset"/></td>
</tr>
</table>
</div>
<div class="section">
<h2>Table key</h2>
<table class="key">
<tr>
<td>Raw Density</td>
<td>Average number of clusters per square mm</td>
</tr>
<tr>
<td>Pass Filter</td>
<td>Fraction of sequences that passed Illumina's chastity filter. Only the sequences that passed the filter are reported</td>
</tr>
<tr>
<td>Yield PF</td>
<td>Total number of bases from pass filter reads</td>
</tr>
<tr>
<td>Clusters PF</td>
<td>Number of clusters (sequences) pass filter</td>
</tr>
<tr>
<td>Q≥30</td>
<td>Fraction of all pass filter bases with Q-score ≥30</td>
</tr>
<tr>
<td>Yield Q≥30</td>
<td>Number of bases with Q-score ≥30</td>
</tr>
<tr>
<td>MeanQ</td>
<td>Mean Q-score over all sequences (±Standard deviation)</td>
</tr>
<tr>
<td>PhiX Error</td>
<td>Fraction of mismatch bases in the spike in phage PhiX control sequences (±Standard deviation)</td>
</tr>
<tr>
<td>Q-score per base A/C/G/T</td>
<td>Mean Q-score for each base (±Standard deviation)</td>
</tr>
<tr>
<td>Tag</td>
<td>The index tag used to identify the sample</td>
</tr>
<tr>
<td>Library</td>
<td>Name of sequencing library</td>
</tr>
<tr>
<td>Insert size</td>
<td>Size of sequenced fragments (excluding adaptors) from bioanalyzer. Peak and range.</td>
</tr>
<tr>
<td>Fraction of lane</td>
<td>Yield for sample compared to the total yield of the lane in which it was sequenced</td>
</tr>
<tr>
<td>Tags with error</td>
<td>Fraction of sequences identified as belonging to the sample containing an error in the tag sequence.(As the tags differ with at least two bases, an error of one base is tolerated in demultiplexing.)</td>
</tr>
<tr>
<td>Q-score distribution</td>
<td>A plot showing the distribution of Q-scores per cycle</td>
</tr>
<tr>
<td>Base composition</td>
<td>Plot on the relative fraction of each base per cycle</td>
</tr>
<tr>
<td>GC distribution</td>
<td>Distribution of GC-content in the sequenced fragments</td>
</tr>
<tr>
<td>Contiguous Length with Q≥30</td>
<td>Plot on the length distribution of the longest contiguous stretch of bases with Q-score < 30</td>
</tr>
<tr>
<td>Duplicates</td>
<td>Frequency of duplicated sequences. The numbers are estimated by following the first 100,000 unique sequences through the whole file.
Identity is based on the first 50 bases.</td>
</tr>
<tr>
<td>Adapter sequences</td>
<td>Cumulative fraction of sequences matching the adapter sequence, starting at cycle X. The match must be at least 6 bases, have at most 1 mismatch per 10 bases and extend to the end of the read or adapter sequence.</td>
</tr>
</table>
</div>
</div>
<div>
<div class="section">
<h2>Files</h2>
<p>There is one directory per sample which contains gzip compressed <a href="http://en.wikipedia.org/wiki/FASTQ_format">FastQ-files</a>. These files are named according to the pattern Sample_Tag_Lane_Read.fastq.gz. The Q-score offset used for ASCII encoding in the FastQ-files is specified in the above table with run parameters.</p>
<p>The directory Plots contains the plots and the underlying data and gnuplot scripts for the plots presented on this page. The plots are divided into one directory per sample plus one directory for lane aggregate plots. The files are named according to Tag-Lane-Read-PlotType*.</p>
<p>report.xml contains these numbers presented in here in xml format</p>
<p>report.xsl is the template used for displaying the data in the xml file as you see it now</p>
<p>report.html is the result of applying the xsl document to the xml data, and is probably the file you opened in your browser</p>
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</body>
</html>
</xsl:template>
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