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installation.html
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<title>ChIP-seq workflow in KNIME - Installation</title>
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<h1>ChIP-seq workflow in KNIME - Installation</h1>
<p>
In this tutorial you will learn how to install the ChIP-seq workflow in KNIME including all required tools.
</p>
<p>
This tutorial is subdivided into the following sections:
<ul>
<li><a href="#installation_knime" >Installation of KNIME</a></li>
<li><a href="#installation_external_tools" >Installation of external tools</a></li>
<ul>
<li><a href="#installation_fastqc" >FastaQC</a></li>
<li><a href="#installation_flexbar" >flexbar</a></li>
<li><a href="#installation_bowtie" >bowtie</a></li>
<li><a href="#installation_yara" >YARA</a></li>
<li><a href="#installation_samtools" >samtools</a></li>
<li><a href="#installation_cross_correlation" >Cross-correlation method</a></li>
<li><a href="#installation_bedtools" >bedtools</a></li>
<li><a href="#installation_ucsc_bedGraphToBigWig" >UCSC's bedGraphToBigWig</a></li>
<li><a href="#installation_macs2" >MACS2</a></li>
<li><a href="#installation_q" >Q</a></li>
</ul>
</ul>
</p>
<h2 id="installation_knime">Installation of KNIME</h2>
<p>
Go here: <a href="https://tech.knime.org/installation-0" target="_knime">KNIME</a>
</p>
<h2 id="installation_external_tools">Installation of external tools</h2>
<h3 id="installation_fastqc">FastaQC - Quality control</h3>
<p>
Go here: <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" target="_fastqc">FastaQC</a>
</p>
<h3 id="installation_flexbar">flexbar - Adapter clipping</h3>
<p>
Go here: <a href="https://github.com/seqan/flexbar" target="_flexbar">flexbar</a>
</p>
<h3 id="installation_bowtie">bowtie - Read mapping</h3>
<p>
Go here: <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.2/" target="_bowtie">bowtie</a>
</p>
<h3 id="installation_yara">YARA - Read mapping</h3>
<p>
Go here: <a href="http://www.seqan.de/projects/yara/" target="_yara">YARA</a>
</p>
<pre><code>echo "Hallo"</code></pre>
<h3 id="installation_samtools">samtools - SAM/BAM file utilities</h3>
<p>
Go here: <a href="http://samtools.sourceforge.net/" target="_samtools">samtools</a>
</p>
<h3 id="installation_cross_correlation">Cross-correlation method - Quality control</h3>
<p>
Original without NSC, RSC, PDC: <a href="http://compbio.med.harvard.edu/Supplements/ChIP-seq/" target="_spp">SPP</a>
</p>
<p>
Modified/extended with NSC, RSC, PDC: <a href="https://code.google.com/archive/p/phantompeakqualtools/" target="_phantompeakqualtools">phantompeakqualtools</a>
</p>
<h3 id="installation_bedtools">bedtools - BED file utilities</h3>
<p>
Go here: <a href="http://bedtools.readthedocs.org/en/latest/content/installation.html" target="_bedtools">bedtools</a>
</p>
<h3 id="installation_ucsc_bedGraphToBigWig">UCSC's bedGraphToBigWig - Converter</h3>
<p>
Go here: <a href="http://hgdownload.cse.ucsc.edu/admin/exe/" target="_ucsc_utilities">UCSC's command-line utilities</a>
</p>
<h3 id="installation_macs2">MACS2 - Peak calling</h3>
<p>
Go here: <a href="https://github.com/taoliu/MACS/blob/master/INSTALL.rst" target="_macs2">MACS2</a>
</p>
<h3 id="installation_q">Q - Peak calling</h3>
<p>
Go here: <a href="http://charite.github.io/Q/" target="_macs2">Q</a>
</p>
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