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<!doctype html>
<html>
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="chrome=1">
<title>NGS by ngscourse</title>
<link rel="stylesheet" href="stylesheets/styles.css">
<link rel="stylesheet" href="stylesheets/pygment_trac.css">
<script src="javascripts/scale.fix.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no">
<!--[if lt IE 9]>
<script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->
</head>
<body>
<div class="wrapper">
<header>
<h1 class="header">NGS</h1>
<p class="header">data analysis course</p>
<ul>
<li><a class="buttons github" href="https://github.com/ngscourse">GitHub Profile</a></li>
</ul>
</header>
<section>
<h1>
<a name="ngs-data-analysis-course" class="anchor" href="#ngs-data-analysis-course"><span class="octicon octicon-link"></span></a>NGS Data Analysis Course</h1>
<h3>
<a name="introduction-to-linux-systems" class="anchor" href="#introduction-to-linux-systems"><span class="octicon octicon-link"></span></a>Introduction to Linux systems</h3>
<h3>
<a name="introduction-to-ngs-technologies" class="anchor" href="#introduction-to-ngs-technologies"><span class="octicon octicon-link"></span></a>Introduction to NGS technologies</h3>
<h3>
<a name="quality-control-for-ngs-raw-data" class="anchor" href="#quality-control-for-ngs-raw-data"><span class="octicon octicon-link"></span></a>Quality control for NGS raw data</h3>
<ul>
<li>
<a href="COURSE_MATERIALS/rna-seq/slides/slides.pdf">Slides</a> - <a href="COURSE_MATERIALS/rna-seq/examples/example.html">Practical exercise 1: fastQC</a> - Practical exercise 2: cutadapt</li>
</ul><h3>
<a name="mapping-reads-to-a-reference-genome" class="anchor" href="#mapping-reads-to-a-reference-genome"><span class="octicon octicon-link"></span></a>Mapping reads to a reference genome</h3>
<h3>
<a name="visualization-of-ngs-data" class="anchor" href="#visualization-of-ngs-data"><span class="octicon octicon-link"></span></a>Visualization of NGS data</h3>
<ul>
<li>
<a href="COURSE_MATERIALS/visualization/slides/2014-Cambridge_visualisation.pdf">Slides</a> || <a href="COURSE_MATERIALS/visualization/example/010_example.html">Practical exercise 1</a> || <a href="COURSE_MATERIALS/visualization/example/020_example.html">Practical exercise 2</a>
</li>
</ul><h3>
<a name="variant-calling" class="anchor" href="#variant-calling"><span class="octicon octicon-link"></span></a>Variant calling</h3>
<h3>
<a name="variant-annotation" class="anchor" href="#variant-annotation"><span class="octicon octicon-link"></span></a>Variant annotation</h3>
<h3>
<a name="association-studies" class="anchor" href="#association-studies"><span class="octicon octicon-link"></span></a>Association studies</h3>
<h3>
<a name="rna-seq-data-processing" class="anchor" href="#rna-seq-data-processing"><span class="octicon octicon-link"></span></a>RNA-Seq data processing</h3>
<h3>
<a name="rna-seq-data-analysis" class="anchor" href="#rna-seq-data-analysis"><span class="octicon octicon-link"></span></a>RNA-Seq data analysis</h3>
<h3>
<a name="functional-analysis" class="anchor" href="#functional-analysis"><span class="octicon octicon-link"></span></a>Functional analysis</h3>
</section>
<footer>
<p><small>Hosted on <a href="http://pages.github.com">GitHub Pages</a> using the Dinky theme</small></p>
</footer>
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