forked from ngs-course/ngs-course.github.io
-
Notifications
You must be signed in to change notification settings - Fork 0
/
index.html
147 lines (112 loc) · 8.17 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
<!DOCTYPE html>
<html>
<head>
<meta charset='utf-8' />
<meta http-equiv="X-UA-Compatible" content="chrome=1" />
<meta name="description" content="NGS course : An introductory course about NGS data analysis" />
<link rel="stylesheet" type="text/css" media="screen" href="stylesheets/stylesheet.css">
<title>NGS course</title>
</head>
<body>
<!-- HEADER -->
<div id="header_wrap" class="outer">
<header class="inner">
<a id="forkme_banner" href="https://github.com/ngs-course">View on GitHub</a>
<h1 id="project_title">NGS course</h1>
<h2 id="project_tagline">An introductory course about NGS data analysis</h2>
</header>
</div>
<!-- MAIN CONTENT -->
<div id="main_content_wrap" class="outer">
<section id="main_content" class="inner">
<h1>
<a name="overview" class="anchor" href="#overview"><span class="octicon octicon-link"></span></a>Overview</h1>
<p>Welcome to this introductory NGS data analysis course. During this course you will learn the basics of NGS data analysis in a Linux environment using most currently used software and best practices will be explained. This course is focused in NGS data alignment for both DNA and RNA (RNA-seq), variant calling, differential expression analysis and data visualization.</p>
<p>This is course is scheduled for a 3 days and assumes a very basic knowledge of NGS data analysis and Linux. All materials in this is course are free and open, feel free to reuse them as you want. Data for the tutorials are available in our <a href="https://www.dropbox.com/sh/4qkqch7gyt888h7/AABD_i9ShwryfAqGeJ0yqqF3a">DropBox folder</a>.</p>
<h1>
<a name="schedule" class="anchor" href="#schedule"><span class="octicon octicon-link"></span></a>Schedule</h1>
<h2>
<a name="day-1" class="anchor" href="#day-1"><span class="octicon octicon-link"></span></a>Day 1</h2>
<p>During this first day we will focus in a NGS data introduction and preparing the data for their analysis. The course starts with a short presentation and a NGS data and GNU/Linux shell introduction. Then we will start working and preparing the data: <em>Quality Control</em> (QC) and <em>NGS data alignment</em>.</p>
<h3>
<a name="presentation" class="anchor" href="#presentation"><span class="octicon octicon-link"></span></a>Presentation</h3>
<ul>
<li>Presentation [<a href="Course_Materials/presentation/presentation_mda14.pdf">PDF</a> | <a href="Course_Materials/presentation/presentation_mda14.odp">OpenOffice</a>]</li>
</ul><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>
<p>Very brief overview about NGS technologies and some concepts.</p>
<ul>
<li><a href="Course_Materials/intro-ngs/ngs_introduction_mda14.pdf">Presentation</a></li>
</ul><h3>
<a name="introduction-to-gnulinux-shell" class="anchor" href="#introduction-to-gnulinux-shell"><span class="octicon octicon-link"></span></a>Introduction to GNU/Linux shell</h3>
<ul>
<li>Presentation [<a href="Course_Materials/intro-linux/intro_Linux_mda14.pdf">PDF</a> | <a href="Course_Materials/intro-linux/intro_Linux_mda14.odp">OpenOffice</a>]</li>
</ul><h3>
<a name="quality-control-for-ngs-raw-data-fastq" class="anchor" href="#quality-control-for-ngs-raw-data-fastq"><span class="octicon octicon-link"></span></a>Quality control for NGS raw data (FASTQ)</h3>
<ul>
<li>
<a href="Course_Materials/quality_control/presentation/quality_control_presentation.pdf">Presentation</a> - <a href="Course_Materials/quality_control/tutorial/quality_control.html">Tutorial</a> - <a href="https://www.dropbox.com/sh/4qkqch7gyt888h7/AAAqebBSC6JgDGq4emwNORCaa/quality_control">Data</a>
</li>
</ul><h3>
<a name="dna-and-rna-seq-read-alignment" class="anchor" href="#dna-and-rna-seq-read-alignment"><span class="octicon octicon-link"></span></a>DNA and RNA-seq read alignment</h3>
<ul>
<li>Presentation [<a href="Course_Materials/alignment/presentation/ngs-read-mapping-imedina-mda14.pdf">PDF</a> | <a href="Course_Materials/alignment/presentation/ngs-read-mapping-imedina-mda14.odp">OpenOffice</a>] - <a href="Course_Materials/alignment/tutorial/example.html">Tutorial</a>
</li>
</ul><h2>
<a name="day-2" class="anchor" href="#day-2"><span class="octicon octicon-link"></span></a>Day 2</h2>
<p>During the second day we will focus on <em>Variant Calling</em> and <em>Data Visualization</em> of DNA and RNA-seq alignments together with VCF files. </p>
<h3>
<a name="ngs-data-visualization" class="anchor" href="#ngs-data-visualization"><span class="octicon octicon-link"></span></a>NGS data Visualization</h3>
<ul>
<li>
<a href="Course_Materials/visualization/presentation/2014-Cambridge_visualisation.pdf">Presentation</a> || <a href="Course_Materials/visualization/tutorial/000_example.html">Guided example</a> || <a href="Course_Materials/visualization/tutorial/010_example.html">Tutorial 1</a> || <a href="Course_Materials/visualization/tutorial/020_example.html">Tutorial 2</a>
</li>
</ul><h3>
<a name="variant-calling-analysis" class="anchor" href="#variant-calling-analysis"><span class="octicon octicon-link"></span></a>Variant calling analysis</h3>
<ul>
<li>
<a href="Course_Materials/variant_calling/presentation/2014-Cambridge_variant_calling.pdf">Presentation</a> || <a href="Course_Materials/variant_calling/tutorial/010_example.html">Tutorial 1</a> || <a href="Course_Materials/variant_calling/tutorial/020_example.html">Tutorial 2</a> || <a href="Course_Materials/variant_calling/tutorial/030_example.html">Tutorial 3</a>
</li>
</ul><h3>
<a name="variant-annotation" class="anchor" href="#variant-annotation"><span class="octicon octicon-link"></span></a>Variant annotation</h3>
<ul>
<li>
<a href="Course_Materials/variant_annotation/presentation/2014-Cambridge_variant_annotation.pdf">Presentation</a> || <a href="Course_Materials/variant_annotation/tutorial/annovar.html">Annovar</a> || <a href="Course_Materials/variant_annotation/tutorial/hpg-variant.html">HPG-Variant</a>
</li>
</ul><h3>
<a name="variant-prioritization" class="anchor" href="#variant-prioritization"><span class="octicon octicon-link"></span></a>Variant prioritization</h3>
<ul>
<li><a href="Course_Materials/variant_prioritization/presentation/2014-Cambridge_variant_prioritization.pdf">Presentation</a></li>
</ul><h2>
<a name="day-3" class="anchor" href="#day-3"><span class="octicon octicon-link"></span></a>Day 3</h2>
<h3>
<a name="association-studies" class="anchor" href="#association-studies"><span class="octicon octicon-link"></span></a>Association studies</h3>
<ul>
<li>
<a href="Course_Materials/association_studies/presentation/association_studies_presentation.pdf">Presentation</a> - <a href="Course_Materials/association_studies/tutorial/association_studies.html">Tutorial</a>
</li>
</ul><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>
<ul>
<li>
<a href="Course_Materials/rna_seq/presentation/rna_seq.pdf">Presentation</a> - <a href="Course_Materials/rna_seq/tutorial/rna_seq.html">Tutorial</a> - <a href="https://www.dropbox.com/sh/4qkqch7gyt888h7/AAB77HfUPkiXBj1MmshjyKtYa/rna_seq">Data</a>
</li>
</ul><h3>
<a name="functional-analysis" class="anchor" href="#functional-analysis"><span class="octicon octicon-link"></span></a>Functional analysis</h3>
<ul>
<li>
<a href="Course_Materials/functional/presentation/babelomics_data_analysis.pdf">Presentation</a> - <a href="http://bioinfo.cipf.es/babelomicstutorial/">Tutorial</a>
</li>
</ul><hr><h1>
<a name="about" class="anchor" href="#about"><span class="octicon octicon-link"></span></a>About</h1>
<p>This course is usually carried out by experienced researchers from CIPF and EMBL-EBI. You can ask any question to David Montaner (<a href="mailto:[email protected]">[email protected]</a>), Marta Bleda (<a href="mailto:[email protected]">[email protected]</a>) and Ignacio Medina (<a href="mailto:[email protected]">[email protected]</a>).</p>
</section>
</div>
<!-- FOOTER -->
<div id="footer_wrap" class="outer">
<footer class="inner">
<p>Published with <a href="http://pages.github.com">GitHub Pages</a></p>
</footer>
</div>
</body>
</html>