https://firas.phd/tags/rna-seq/ Recent content in RNA-Seq on Firas Sadiyah https://firas.phd/favicon.png https://firas.phd/favicon.png Hugo en Tue, 23 Jan 2024 14:57:54 +0000 https://firas.phd/posts/dapars/ Sun, 19 Mar 2017 12:00:00 +0000 https://firas.phd/posts/dapars/ <p>A colleague of mine asked me for help in using <a href="https://github.com/FirasSadiyah/dapars">DaPars</a> for analysing alternative polyadenylation in their RNA-seq dataset. So, I thought to write a short post here to describe how I use it.</p> <p>From <a href="http://www.nature.com/articles/ncomms6274">Xia <em>et al</em>. 2014</a></p> <blockquote> <p>Here we develop a novel bioinformatics algorithm (DaPars) for the de novo identification of dynamic APAs from standard RNA-seq.</p></blockquote> <h1 id="installation">Installation</h1> <p>Download the source files of DaPars from <a href="https://github.com/ZhengXia/dapars">GitHub</a> and extract the files:</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-bash" data-lang="bash"><span class="line"><span class="ln">1</span><span class="cl">$ tar zxvf DaPars-VERSION.tar.gz </span></span></code></pre></div><h1 id="input-files">Input files</h1> <p>You can find more details on the <a href="http://lilab.research.bcm.edu/dldcc-web/lilab/zheng/DaPars_Documentation/html/DaPars.html">documentation page</a>, but in essence, DaPars requires the following files:</p>