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<h1 class="title"><a href="http://ngscourse.github.io/">NGS data analysis course</a></h1>
<h2 class="author"><strong>Visualization of mapped reads</strong></h2>
<h3 class="date"><em>(updated 26-02-2014)</em></h3>
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<h1 id="preliminaries">Preliminaries</h1>
<h2 id="software-used-in-this-practical">Software used in this practical:</h2>
<ul>
<li><a href="http://www.broadinstitute.org/igv/home" title="IGV">IGV</a> : The Integrative Genomics Viewer is a program for reading several types of indexed database information, including mapped reads and variant calls, and displaying them on a reference genome. It is invaluable as a tool for viewing and interpreting the “raw data” of many NGS data analysis pipelines.</li>
<li><a href="http://samtools.sourceforge.net/" title="samtools">samtools</a> : SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.</li>
</ul>
<h2 id="file-formats-explored">File formats explored:</h2>
<ul>
<li><a href="http://samtools.sourceforge.net/SAMv1.pdf">SAM</a></li>
<li><a href="http://www.broadinstitute.org/igv/bam">BAM</a></li>
</ul>
<h1 id="exercise-1-visualizing-sequencing-data">Exercise 1: Visualizing sequencing data</h1>
<p>In the following <strong>folder</strong> you wil find mapped sequencing data from a CEU trio (father, mother and child) from the 1000 Genomes Project:</p>
<pre><code>cd /home/participant/cambridge_mda14/visualization/example_1</code></pre>
<p>These datasets contain reads only for the <a href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000204681;r=6:29523406-29601753">GABBR1</a> gene.</p>
<h2 id="creating-indexed-files">Creating indexed files</h2>
<p>Use <code>samtools</code> to index the bam files:</p>
<pre><code>samtools index NA12878_child.bam
samtools index NA12891_dad.bam
samtools index NA12892_mom.bam</code></pre>
<h2 id="run-igv">Run IGV</h2>
<p>You can run this command from the terminal: igv</p>
<p>or you can also use the link in your Desktop.</p>
<h2 id="downolad-a-referece-genome">Downolad a referece genome</h2>
<p>Run just in the case you do not have downloaded Human hg19 genome before:</p>
<ul>
<li>Go to <code>Genomes</code> –&gt; <code>Load Genome From Server...</code> Select <strong>Human hg19</strong></li>
</ul>
<h2 id="loading-and-browsing-files">Loading and browsing files</h2>
<ul>
<li>Go to <code>File</code> –&gt; <code>Load from file...</code> Select NA12878_child.bam, NA12891_dad.bam and NA12892_mom.bam</li>
</ul>
<p><strong>Steps:</strong></p>
<ol style="list-style-type: decimal">
<li>Enter the name of our gene (<em><strong>GABBR1</strong></em>) in the search box and hit <code>Go</code>.</li>
<li>Zoom in until you find some SNPs - they might be in exons or introns.</li>
<li>Identify at least one example of a short insertion variant and deletion arround exon 4.</li>
<li>Load and look at the SNP track: <code>File</code> –&gt; <code>Load from server</code> –&gt; <code>Annotations</code> –&gt; <code>Variants and Repeats</code> –&gt; <code>dbSNP</code></li>
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