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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Training course for Exome sequencing</title>
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<body>
<div class="reveal">
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<div class="slides">
<section data-markdown>
<script type="text/template">
## Welcome!
<img src="../../shared/images/GTNLogo1000.png" alt="GTNLogo1000"
class="no-border" width=30%/>
The easiest way to **navigate** this slide deck
is **by hitting `[space]` on your keyboard**
You can also navigate with arrow keys, but be careful because some
slides can be nested inside of each other (vertically)
</script>
</section>
<section data-markdown>
<script type="text/template">
# Exome sequence data analysis
</script>
</section>
<section>
<section data-markdown>
<script type="text/template">
### Exome sequencing
= Whole exome sequencing (WES or WXS)
Sequencing of all expressed protein-coding genes in a genome
</script>
</section>
<section data-markdown>
<script type="text/template">
### Exome in Humans
- ~180,000 exons
- 1% of the human genome
- ~30 million base pairs
</script>
</section>
<section data-markdown>
<script type="text/template">
### Goal of exome sequencing
Identify genetic variation that is responsible for both Mendelian
and common diseases without the high costs associated with
whole-genome sequencing
<aside class="notes">
Exome sequencing is the most efficient way to identify the
genetic variants in all of an individual's genes
</aside>
</script>
</section>
<section data-markdown>
<script type="text/template">
### Limits
Exome sequencing can not identify genetic variation in
- All genes
- Mitochondrial genes
- “Structural variants”
- Triplet repeat disorders
- Other copy number variants
- Introns
- “Uniparental disomy”
- Control sequences
- Epigenetic changes
- Gene-gene (epistatic) interactions
</script>
</section>
</section>
<section>
<section data-markdown>
<script type="text/template">
## 2 tutorials for training on exome sequencing data analysis
</script>
</section>
<section data-markdown>
<script type="text/template">
### Same goal
Identify and annotate genetic variants in a family with two
parents and a child exome data
</script>
</section>
<section data-markdown>
<script type="text/template">
### Similar data analysis approach
<img src="../images/genVAST.png" alt="Exome sequencing analysis pipeline"
class="no-border" width=50%/>
</script>
</section>
<section data-markdown>
<script type="text/template">
### 2 tutorials
- [Introductory tutorial](http://galaxyproject.github.io/training-material/Exome-Seq/tutorials/Exome-Seq.html)
- [Detailed tutorial](http://galaxyproject.github.io/training-material/Exome-Seq/tutorials/Diploid-variant-calling.html)
</script>
</section>
</section>
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