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Added Table of Contents and easy navigation to documentation. #67

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a176fb1
added link to basic operations
alanhoyle Dec 3, 2020
020da23
Update 1.1 What is FastQC.html
alanhoyle Dec 3, 2020
271787b
Added Doc ToC, minor html changes
alanhoyle Dec 3, 2020
0d0ac46
Merge branch 's-andrews:master' into master
alanhoyle Jul 14, 2021
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38 changes: 34 additions & 4 deletions Help/1 Introduction/1.1 What is FastQC.html
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<html>

<head>
<title>What is FastQC?</title>
<title>1.1 - What is FastQC?</title>
<style type="text/css">
body {
font-family: sans-serif;
}
</style>
</head>
<body>
<h1>What is FastQC</h1>
<h1>1.1 - What is FastQC</h1>
<p>
Modern high throughput sequencers can generate hundreds of millions of sequences
in a single run. Before analysing this sequence to draw biological conclusions
Expand All @@ -18,7 +18,7 @@ <h1>What is FastQC</h1>
may affect how you can usefully use it.
</p>
<p>
Most sequencers will generate a QC report as part of their analysis pipeline,
Most sequencers will generate a QC report as part of their analysis pipeline,
but this is usually only focused on identifying problems which were generated
by the sequencer itself. FastQC aims to provide a QC report which can spot
problems which originate either in the sequencer or in the starting library
Expand All @@ -31,6 +31,36 @@ <h1>What is FastQC</h1>
for integrating into a larger analysis pipeline for the systematic processing
of large numbers of files.
</p>
<hr />
<ul>
<li><a href="../">FastQC Help Top</a>
<ul>
<li><a href="../1%20Introduction/1.1%20What%20is%20FastQC.html">1.1 What is FastQC.html</a></li>
<li><a href="../2%20Basic%20Operations/">2 Basic Operations</a>
<ul>
<li><a href="../2%20Basic%20Operations/2.1%20Opening%20a%20sequence%20file.html">2.1 Opening a sequence file</a></li>
<li><a href="../2%20Basic%20Operations/2.2%20Evaluating%20Results.html">2.2 Evaluating Results</a></li>
<li><a href="../2%20Basic%20Operations/2.3%20Saving%20a%20Report.html">2.3 Saving a Report</a></li>
</ul>
</li>
<li><a href="../3%20Analysis%20Modules/">3 Analysis Modules</a>
<ul>
<li><a href="../3%20Analysis%20Modules/1%20Basic%20Statistics.html">3.1 Basic Statistics</a></li>
<li><a href="../3%20Analysis%20Modules/2%20Per%20Base%20Sequence%20Quality.html">3.2 Per Base Sequence Quality</a></li>
<li><a href="../3%20Analysis%20Modules/3%20Per%20Sequence%20Quality%20Scores.html">3.3 Per Sequence Quality Scores</a></li>
<li><a href="../3%20Analysis%20Modules/4%20Per%20Base%20Sequence%20Content.html">3.4 Per Base Sequence Content</a></li>
<li><a href="../3%20Analysis%20Modules/5%20Per%20Sequence%20GC%20Content.html">3.5 Per Sequence GC Content</a></li>
<li><a href="../3%20Analysis%20Modules/6%20Per%20Base%20N%20Content.html">3.6 Per Base N Content</a></li>
<li><a href="../3%20Analysis%20Modules/7%20Sequence%20Length%20Distribution.html">3.7 Sequence Length Distribution</a></li>
<li><a href="../3%20Analysis%20Modules/8%20Duplicate%20Sequences.html">3.8 Duplicate Sequences</a></li>
<li><a href="../3%20Analysis%20Modules/9%20Overrepresented%20Sequences.html">3.9 Overrepresented Sequences</a></li>
<li><a href="../3%20Analysis%20Modules/10%20Adapter%20Content.html">3.10 Adapter Content</a></li>
<li><a href="../3%20Analysis%20Modules/11%20Kmer%20Content.html">3.11 Kmer Content</a></li>
<li><a href="../3%20Analysis%20Modules/12%20Per%20Tile%20Sequence%20Quality.html">3.12 Per Tile Sequence Quality</a></li>
</ul>
</li>
</ul>
</ul>
</body>

</html>
</html>
46 changes: 37 additions & 9 deletions Help/2 Basic Operations/2.1 Opening a sequence file.html
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<html>

<head>
<title>Opening a FastQ file</title>
<title>2.1 - Opening a FastQ file</title>
<style type="text/css">
body {
font-family: sans-serif;
}
</style>
</head>
<body>
<h1>Opening a Sequence file</h1>
<h1>2.1 - Opening a Sequence file</h1>
<p>
To open one or more Sequence files interactively simply run the
program and select File &gt; Open. You can then select the files
Expand All @@ -34,7 +34,7 @@ <h1>Opening a Sequence file</h1>
<li>BAM</li>
<li>SAM/BAM Mapped only (normally used for colorspace data)</li>
</ul>

<p>
* Casava fastq format is the same as regular fastq except that
the data is usually split across multiple files for a single sample.
Expand All @@ -44,20 +44,48 @@ <h1>Opening a Sequence file</h1>
In Casava mode the program will exclude these flagged sequences from
the report.
</p>

<p>
By default FastQC will try to guess the file format from the name
of the input file. Anything ending in .sam or .bam will be
of the input file. Anything ending in .sam or .bam will be
opened as a SAM/BAM file (using all sequences, mapped and unmapped)
, and everything else will be treated as FastQ format. If you want
, and everything else will be treated as FastQ format. If you want
to override this detection and specify the file format manually
then you can use the drop down file filter in the file chooser to
select the type of file you're going to load. You need to use the
select the type of file you're going to load. You need to use the
drop down selector to make the program use the Mapped BAM or Casava
file modes as these won't be selected automatically.
</p>


<hr />
<ul>
<li><a href="../">FastQC Help Top</a>
<ul>
<li><a href="../1%20Introduction/1.1%20What%20is%20FastQC.html">1.1 What is FastQC.html</a></li>
<li><a href="../2%20Basic%20Operations/">2 Basic Operations</a>
<ul>
<li><a href="../2%20Basic%20Operations/2.1%20Opening%20a%20sequence%20file.html">2.1 Opening a sequence file</a></li>
<li><a href="../2%20Basic%20Operations/2.2%20Evaluating%20Results.html">2.2 Evaluating Results</a></li>
<li><a href="../2%20Basic%20Operations/2.3%20Saving%20a%20Report.html">2.3 Saving a Report</a></li>
</ul>
</li>
<li><a href="../3%20Analysis%20Modules/">3 Analysis Modules</a>
<ul>
<li><a href="../3%20Analysis%20Modules/1%20Basic%20Statistics.html">3.1 Basic Statistics</a></li>
<li><a href="../3%20Analysis%20Modules/2%20Per%20Base%20Sequence%20Quality.html">3.2 Per Base Sequence Quality</a></li>
<li><a href="../3%20Analysis%20Modules/3%20Per%20Sequence%20Quality%20Scores.html">3.3 Per Sequence Quality Scores</a></li>
<li><a href="../3%20Analysis%20Modules/4%20Per%20Base%20Sequence%20Content.html">3.4 Per Base Sequence Content</a></li>
<li><a href="../3%20Analysis%20Modules/5%20Per%20Sequence%20GC%20Content.html">3.5 Per Sequence GC Content</a></li>
<li><a href="../3%20Analysis%20Modules/6%20Per%20Base%20N%20Content.html">3.6 Per Base N Content</a></li>
<li><a href="../3%20Analysis%20Modules/7%20Sequence%20Length%20Distribution.html">3.7 Sequence Length Distribution</a></li>
<li><a href="../3%20Analysis%20Modules/8%20Duplicate%20Sequences.html">3.8 Duplicate Sequences</a></li>
<li><a href="../3%20Analysis%20Modules/9%20Overrepresented%20Sequences.html">3.9 Overrepresented Sequences</a></li>
<li><a href="../3%20Analysis%20Modules/10%20Adapter%20Content.html">3.10 Adapter Content</a></li>
<li><a href="../3%20Analysis%20Modules/11%20Kmer%20Content.html">3.11 Kmer Content</a></li>
<li><a href="../3%20Analysis%20Modules/12%20Per%20Tile%20Sequence%20Quality.html">3.12 Per Tile Sequence Quality</a></li>
</ul>
</li>
</ul>
</ul>
</body>

</html>
34 changes: 32 additions & 2 deletions Help/2 Basic Operations/2.2 Evaluating Results.html
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<html>

<head>
<title>Evaluating Results</title>
<title>2.2 - Evaluating Results</title>
<style type="text/css">
body {
font-family: sans-serif;
}
</style>
</head>
<body>
<h1>Evaluating Results</h1>
<h1>2.2 - Evaluating Results</h1>
<p>
The analysis in FastQC is performed by a series of analysis
modules. The left hand side of the main interactive display
Expand All @@ -33,5 +33,35 @@ <h1>Evaluating Results</h1>
Specific guidance on how to interpret the output of each
module can be found in the modules section of the help.
</p>
<hr />
<ul>
<li><a href="../">FastQC Help Top</a>
<ul>
<li><a href="../1%20Introduction/1.1%20What%20is%20FastQC.html">1.1 What is FastQC.html</a></li>
<li><a href="../2%20Basic%20Operations/">2 Basic Operations</a>
<ul>
<li><a href="../2%20Basic%20Operations/2.1%20Opening%20a%20sequence%20file.html">2.1 Opening a sequence file</a></li>
<li><a href="../2%20Basic%20Operations/2.2%20Evaluating%20Results.html">2.2 Evaluating Results</a></li>
<li><a href="../2%20Basic%20Operations/2.3%20Saving%20a%20Report.html">2.3 Saving a Report</a></li>
</ul>
</li>
<li><a href="../3%20Analysis%20Modules/">3 Analysis Modules</a>
<ul>
<li><a href="../3%20Analysis%20Modules/1%20Basic%20Statistics.html">3.1 Basic Statistics</a></li>
<li><a href="../3%20Analysis%20Modules/2%20Per%20Base%20Sequence%20Quality.html">3.2 Per Base Sequence Quality</a></li>
<li><a href="../3%20Analysis%20Modules/3%20Per%20Sequence%20Quality%20Scores.html">3.3 Per Sequence Quality Scores</a></li>
<li><a href="../3%20Analysis%20Modules/4%20Per%20Base%20Sequence%20Content.html">3.4 Per Base Sequence Content</a></li>
<li><a href="../3%20Analysis%20Modules/5%20Per%20Sequence%20GC%20Content.html">3.5 Per Sequence GC Content</a></li>
<li><a href="../3%20Analysis%20Modules/6%20Per%20Base%20N%20Content.html">3.6 Per Base N Content</a></li>
<li><a href="../3%20Analysis%20Modules/7%20Sequence%20Length%20Distribution.html">3.7 Sequence Length Distribution</a></li>
<li><a href="../3%20Analysis%20Modules/8%20Duplicate%20Sequences.html">3.8 Duplicate Sequences</a></li>
<li><a href="../3%20Analysis%20Modules/9%20Overrepresented%20Sequences.html">3.9 Overrepresented Sequences</a></li>
<li><a href="../3%20Analysis%20Modules/10%20Adapter%20Content.html">3.10 Adapter Content</a></li>
<li><a href="../3%20Analysis%20Modules/11%20Kmer%20Content.html">3.11 Kmer Content</a></li>
<li><a href="../3%20Analysis%20Modules/12%20Per%20Tile%20Sequence%20Quality.html">3.12 Per Tile Sequence Quality</a></li>
</ul>
</li>
</ul>
</ul>
</body>
</html>
41 changes: 35 additions & 6 deletions Help/2 Basic Operations/2.3 Saving a Report.html
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<html>

<head>
<title>Saving a Report</title>
<title>2.3 - Saving a Report</title>
<style type="text/css">
body {
font-family: sans-serif;
}
</style>
</head>
<body>
<h1>Saving a Report</h1>
<h1>2.3 - Saving a Report</h1>
<p>
In addition to providing an interactive report FastQC also
has the option to create an HTML version of this report
Expand All @@ -28,12 +28,41 @@ <h1>Saving a Report</h1>
The HTML file which is saved is a self-contained document with
all of the graphs embedded into it, so you can distribute this
single file. Alongside the HTML file is a zip file (with the
same name as the HTML file, but with .zip added to the end).
same name as the HTML file, but with .zip added to the end).
This file contains the graphs from the report as separate files
but also contains data files which are designed to be easily
parsed to allow for a more detailed and automated evauation of
but also contains data files which are designed to be easily
parsed to allow for a more detailed and automated evauation of
the raw data on which the QC report is built.
</p>

<hr />
<ul>
<li><a href="../">FastQC Help Top</a>
<ul>
<li><a href="../1%20Introduction/1.1%20What%20is%20FastQC.html">1.1 What is FastQC.html</a></li>
<li><a href="../2%20Basic%20Operations/">2 Basic Operations</a>
<ul>
<li><a href="../2%20Basic%20Operations/2.1%20Opening%20a%20sequence%20file.html">2.1 Opening a sequence file</a></li>
<li><a href="../2%20Basic%20Operations/2.2%20Evaluating%20Results.html">2.2 Evaluating Results</a></li>
<li><a href="../2%20Basic%20Operations/2.3%20Saving%20a%20Report.html">2.3 Saving a Report</a></li>
</ul>
</li>
<li><a href="../3%20Analysis%20Modules/">3 Analysis Modules</a>
<ul>
<li><a href="../3%20Analysis%20Modules/1%20Basic%20Statistics.html">3.1 Basic Statistics</a></li>
<li><a href="../3%20Analysis%20Modules/2%20Per%20Base%20Sequence%20Quality.html">3.2 Per Base Sequence Quality</a></li>
<li><a href="../3%20Analysis%20Modules/3%20Per%20Sequence%20Quality%20Scores.html">3.3 Per Sequence Quality Scores</a></li>
<li><a href="../3%20Analysis%20Modules/4%20Per%20Base%20Sequence%20Content.html">3.4 Per Base Sequence Content</a></li>
<li><a href="../3%20Analysis%20Modules/5%20Per%20Sequence%20GC%20Content.html">3.5 Per Sequence GC Content</a></li>
<li><a href="../3%20Analysis%20Modules/6%20Per%20Base%20N%20Content.html">3.6 Per Base N Content</a></li>
<li><a href="../3%20Analysis%20Modules/7%20Sequence%20Length%20Distribution.html">3.7 Sequence Length Distribution</a></li>
<li><a href="../3%20Analysis%20Modules/8%20Duplicate%20Sequences.html">3.8 Duplicate Sequences</a></li>
<li><a href="../3%20Analysis%20Modules/9%20Overrepresented%20Sequences.html">3.9 Overrepresented Sequences</a></li>
<li><a href="../3%20Analysis%20Modules/10%20Adapter%20Content.html">3.10 Adapter Content</a></li>
<li><a href="../3%20Analysis%20Modules/11%20Kmer%20Content.html">3.11 Kmer Content</a></li>
<li><a href="../3%20Analysis%20Modules/12%20Per%20Tile%20Sequence%20Quality.html">3.12 Per Tile Sequence Quality</a></li>
</ul>
</li>
</ul>
</ul>
</body>
</html>
43 changes: 36 additions & 7 deletions Help/3 Analysis Modules/1 Basic Statistics.html
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<html>

<head>
<title>Basic Statistics</title>
<title>3.1 - Basic Statistics</title>
<style type="text/css">
body {
font-family: sans-serif;
}
</style>
</head>
<body>
<h1>Basic Statistics</h1>
<h1>3.1 - Basic Statistics</h1>
<h2>Summary</h2>
<p>
The Basic Statistics module generates some simple composition
Expand All @@ -21,14 +21,14 @@ <h2>Summary</h2>
<li>File type: Says whether the file appeared to contain actual base calls or
colorspace data which had to be converted to base calls</li>
<li>Encoding: Says which ASCII encoding of quality values was found in this
file.
</li><li>Total Sequences: A count of the total number of sequences processed.
file.</li>
<li>Total Sequences: A count of the total number of sequences processed.
There are two values reported, actual and estimated. At the moment these
will always be the same. In the future it may be possible to analyse just
a subset of sequences and estimate the total number, to speed up the analysis,
but since we have found that problematic sequences are not evenly distributed
through a file we have disabled this for now.</li>
<li>Filtered Sequences: If running in Casava mode sequences flagged to be
<li>Filtered Sequences: If running in Casava mode sequences flagged to be
filtered will be removed from all analyses. The number of such sequences
removed will be reported here. The total sequences count above will not include
these filtered sequences and will the number of sequences actually used for the
Expand All @@ -53,6 +53,35 @@ <h2>Common reasons for warnings</h2>
<p>
This module never raises warnings or errors
</p>

<hr />
<ul>
<li><a href="../">FastQC Help Top</a>
<ul>
<li><a href="../1%20Introduction/1.1%20What%20is%20FastQC.html">1.1 What is FastQC.html</a></li>
<li><a href="../2%20Basic%20Operations/">2 Basic Operations</a>
<ul>
<li><a href="../2%20Basic%20Operations/2.1%20Opening%20a%20sequence%20file.html">2.1 Opening a sequence file</a></li>
<li><a href="../2%20Basic%20Operations/2.2%20Evaluating%20Results.html">2.2 Evaluating Results</a></li>
<li><a href="../2%20Basic%20Operations/2.3%20Saving%20a%20Report.html">2.3 Saving a Report</a></li>
</ul>
</li>
<li><a href="../3%20Analysis%20Modules/">3 Analysis Modules</a>
<ul>
<li><a href="../3%20Analysis%20Modules/1%20Basic%20Statistics.html">3.1 Basic Statistics</a></li>
<li><a href="../3%20Analysis%20Modules/2%20Per%20Base%20Sequence%20Quality.html">3.2 Per Base Sequence Quality</a></li>
<li><a href="../3%20Analysis%20Modules/3%20Per%20Sequence%20Quality%20Scores.html">3.3 Per Sequence Quality Scores</a></li>
<li><a href="../3%20Analysis%20Modules/4%20Per%20Base%20Sequence%20Content.html">3.4 Per Base Sequence Content</a></li>
<li><a href="../3%20Analysis%20Modules/5%20Per%20Sequence%20GC%20Content.html">3.5 Per Sequence GC Content</a></li>
<li><a href="../3%20Analysis%20Modules/6%20Per%20Base%20N%20Content.html">3.6 Per Base N Content</a></li>
<li><a href="../3%20Analysis%20Modules/7%20Sequence%20Length%20Distribution.html">3.7 Sequence Length Distribution</a></li>
<li><a href="../3%20Analysis%20Modules/8%20Duplicate%20Sequences.html">3.8 Duplicate Sequences</a></li>
<li><a href="../3%20Analysis%20Modules/9%20Overrepresented%20Sequences.html">3.9 Overrepresented Sequences</a></li>
<li><a href="../3%20Analysis%20Modules/10%20Adapter%20Content.html">3.10 Adapter Content</a></li>
<li><a href="../3%20Analysis%20Modules/11%20Kmer%20Content.html">3.11 Kmer Content</a></li>
<li><a href="../3%20Analysis%20Modules/12%20Per%20Tile%20Sequence%20Quality.html">3.12 Per Tile Sequence Quality</a></li>
</ul>
</li>
</ul>
</ul>
</body>
</html>
</html>
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