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<!DOCTYPE html>
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<!--bookdown:title:start-->
<div id="header">
<h1 class="title">Differential Expression Workshop NCGR</h1>
</div>
<!--bookdown:title:end-->
<!--bookdown:toc:start-->
<div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
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<!--bookdown:toc2:start-->
<ul>
<li><a href="#url-your-book-url-like-httpsbookdown.orgyihuibookdown" id="toc-url-your-book-url-like-httpsbookdown.orgyihuibookdown"><span class="toc-section-number">1</span> url: your book url like https://bookdown.org/yihui/bookdown</a>
<ul>
<li><a href="#getting-started" id="toc-getting-started">Getting Started</a></li>
<li><a href="#prerequisites" id="toc-prerequisites"><span class="toc-section-number">1.1</span> Prerequisites</a></li>
<li><a href="#installs" id="toc-installs"><span class="toc-section-number">1.2</span> Installs</a></li>
<li><a href="#agenda" id="toc-agenda"><span class="toc-section-number">1.3</span> Agenda</a></li>
<li><a href="#connecting-to-the-linux-server" id="toc-connecting-to-the-linux-server"><span class="toc-section-number">1.4</span> Connecting to the linux server</a></li>
</ul></li>
<li><a href="#linux-basics" id="toc-linux-basics"><span class="toc-section-number">2</span> Linux Basics</a>
<ul>
<li><a href="#connecting-to-the-linux-server-1" id="toc-connecting-to-the-linux-server-1"><span class="toc-section-number">2.1</span> Connecting to the linux server</a></li>
<li><a href="#what-are-linux-bash-and-the-ncgr-server" id="toc-what-are-linux-bash-and-the-ncgr-server"><span class="toc-section-number">2.2</span> What are Linux, bash, and the NCGR Server?</a>
<ul>
<li><a href="#a-little-shell-aka-the-prompt-is-the-command-line-interface" id="toc-a-little-shell-aka-the-prompt-is-the-command-line-interface">A little shell… aka the $ prompt is the command line interface</a></li>
<li><a href="#directory-structure" id="toc-directory-structure">Directory Structure</a></li>
<li><a href="#find-the-shell-in-system-youll-use-to-log-into-the-ncgrs-server" id="toc-find-the-shell-in-system-youll-use-to-log-into-the-ncgrs-server"><span class="toc-section-number">2.2.1</span> Find the shell in system you’ll use to log into the NCGR’s server</a></li>
<li><a href="#log-on-to-ncgrs-server" id="toc-log-on-to-ncgrs-server"><span class="toc-section-number">2.2.2</span> Log on to NCGR’s server</a></li>
<li><a href="#now-that-i-logged-on-where-am-i" id="toc-now-that-i-logged-on-where-am-i"><span class="toc-section-number">2.2.3</span> Now that I logged on, where am I?</a></li>
</ul></li>
<li><a href="#linux-basics-part-i" id="toc-linux-basics-part-i"><span class="toc-section-number">2.3</span> Linux basics: Part I:</a>
<ul>
<li><a href="#understanding-directories" id="toc-understanding-directories"><span class="toc-section-number">2.3.1</span> Understanding Directories</a></li>
<li><a href="#listing-options" id="toc-listing-options"><span class="toc-section-number">2.3.2</span> Listing options</a></li>
<li><a href="#navigation" id="toc-navigation"><span class="toc-section-number">2.3.3</span> Navigation</a></li>
<li><a href="#files-creating-with-touch-command" id="toc-files-creating-with-touch-command"><span class="toc-section-number">2.3.4</span> Files: creating with touch command</a></li>
<li><a href="#history-command" id="toc-history-command"><span class="toc-section-number">2.3.5</span> History command</a></li>
<li><a href="#files-creating-by-redirecting-standard-out" id="toc-files-creating-by-redirecting-standard-out"><span class="toc-section-number">2.3.6</span> Files: creating by redirecting standard out</a></li>
<li><a href="#file-name-completion-with-tab" id="toc-file-name-completion-with-tab"><span class="toc-section-number">2.3.7</span> File name completion with tab</a></li>
<li><a href="#files-moving-files-from-one-filename-to-another" id="toc-files-moving-files-from-one-filename-to-another"><span class="toc-section-number">2.3.8</span> Files: moving files from one filename to another</a></li>
<li><a href="#files-copying-files-from-one-filename-to-another" id="toc-files-copying-files-from-one-filename-to-another"><span class="toc-section-number">2.3.9</span> Files: copying files from one filename to another</a></li>
<li><a href="#files-securely-copying-files-between-your-laptop-and-ncgrs-server" id="toc-files-securely-copying-files-between-your-laptop-and-ncgrs-server"><span class="toc-section-number">2.3.10</span> Files: securely copying files between your laptop and NCGRs server</a></li>
<li><a href="#files-and-directories-removing-files-is-deleting-files" id="toc-files-and-directories-removing-files-is-deleting-files"><span class="toc-section-number">2.3.11</span> Files and directories: removing files is deleting files</a></li>
<li><a href="#tool-box-how-to-abort-a-commandprocess" id="toc-tool-box-how-to-abort-a-commandprocess"><span class="toc-section-number">2.3.12</span> Tool box: How to abort a command/process</a></li>
</ul></li>
<li><a href="#linux-basics-part-ii" id="toc-linux-basics-part-ii"><span class="toc-section-number">2.4</span> Linux basics: Part II</a>
<ul>
<li><a href="#files-symbolic-links-and-the-soft-link--s" id="toc-files-symbolic-links-and-the-soft-link--s"><span class="toc-section-number">2.4.1</span> Files: Symbolic links and the soft link (-s)</a></li>
<li><a href="#understanding-a-fasta-file-format" id="toc-understanding-a-fasta-file-format"><span class="toc-section-number">2.4.2</span> Understanding a fasta file format</a></li>
<li><a href="#understanding-fastq-fq-file-format" id="toc-understanding-fastq-fq-file-format"><span class="toc-section-number">2.4.3</span> Understanding fastq (fq) file format</a></li>
<li><a href="#using-grep-global-regular-expression-print-to-extract-metrics" id="toc-using-grep-global-regular-expression-print-to-extract-metrics"><span class="toc-section-number">2.4.4</span> Using grep (global regular expression print) to extract metrics</a></li>
<li><a href="#working-with-compressed-files" id="toc-working-with-compressed-files"><span class="toc-section-number">2.4.5</span> Working with compressed files</a></li>
<li><a href="#start-and-end-symbols" id="toc-start-and-end-symbols"><span class="toc-section-number">2.4.6</span> Start ^ and end $ symbols</a></li>
<li><a href="#files-parsing-and-creating-data-subsets" id="toc-files-parsing-and-creating-data-subsets"><span class="toc-section-number">2.4.7</span> Files: parsing and creating data-subsets</a></li>
<li><a href="#files-parsing-and-creating-data-subsets-1" id="toc-files-parsing-and-creating-data-subsets-1"><span class="toc-section-number">2.4.8</span> Files: parsing and creating data-subsets</a></li>
<li><a href="#files-parsing-and-creating-data-subsets-2" id="toc-files-parsing-and-creating-data-subsets-2"><span class="toc-section-number">2.4.9</span> Files: parsing and creating data-subsets</a></li>
<li><a href="#files-parsing-and-creating-data-subsets-3" id="toc-files-parsing-and-creating-data-subsets-3"><span class="toc-section-number">2.4.10</span> Files: parsing and creating data-subsets</a></li>
<li><a href="#revisiting-table1-and-previous-awk-command" id="toc-revisiting-table1-and-previous-awk-command"><span class="toc-section-number">2.4.11</span> Revisiting table1 and <em>previous</em> awk command</a></li>
<li><a href="#files-stream-editor-sed" id="toc-files-stream-editor-sed"><span class="toc-section-number">2.4.12</span> Files: <strong>S</strong>tream <strong>ED</strong>itor (sed)</a></li>
<li><a href="#the-bash-for-loop" id="toc-the-bash-for-loop"><span class="toc-section-number">2.4.13</span> The Bash “for” Loop</a></li>
<li><a href="#help-with-command-syntax" id="toc-help-with-command-syntax"><span class="toc-section-number">2.4.14</span> Help with command syntax</a></li>
<li><a href="#exercises" id="toc-exercises"><span class="toc-section-number">2.4.15</span> Exercises</a></li>
</ul></li>
<li><a href="#linux-basics-part-iii" id="toc-linux-basics-part-iii"><span class="toc-section-number">2.5</span> Linux basics: Part III</a>
<ul>
<li><a href="#using-the-screen-command" id="toc-using-the-screen-command">Using the Screen Command</a></li>
<li><a href="#exercise-1" id="toc-exercise-1">Exercise</a></li>
<li><a href="#more-exercises" id="toc-more-exercises"><span class="toc-section-number">2.5.1</span> More Exercises</a></li>
</ul></li>
</ul></li>
<li><a href="#sequence-metrics-and-quality-control" id="toc-sequence-metrics-and-quality-control"><span class="toc-section-number">3</span> Sequence metrics and quality Control</a>
<ul>
<li><a href="#the-study-design" id="toc-the-study-design"><span class="toc-section-number">3.1</span> The Study Design</a></li>
<li><a href="#data-access" id="toc-data-access"><span class="toc-section-number">3.2</span> Data Access</a></li>
<li><a href="#fastp-quality-control" id="toc-fastp-quality-control"><span class="toc-section-number">3.3</span> fastp Quality Control</a></li>
<li><a href="#checking-sequence-metrics" id="toc-checking-sequence-metrics"><span class="toc-section-number">3.4</span> Checking Sequence Metrics</a></li>
</ul></li>
</ul>
<!--bookdown:toc2:end-->
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<h1>
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<h1 class="hasAnchor"><span class="header-section-number">1</span> url: your book url like <a href="https://bookdown.org/yihui/bookdown" class="uri">https://bookdown.org/yihui/bookdown</a><a href="#url-your-book-url-like-httpsbookdown.orgyihuibookdown" class="anchor-section" aria-label="Anchor link to header"></a></h1>
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</div>
<div id="prerequisites" class="section level2 hasAnchor" number="1.1">
<h2 class="hasAnchor"><span class="header-section-number">1.1</span> Prerequisites<a href="#prerequisites" class="anchor-section" aria-label="Anchor link to header"></a></h2>
</div>
<div id="installs" class="section level2 hasAnchor" number="1.2">
<h2 class="hasAnchor"><span class="header-section-number">1.2</span> Installs<a href="#installs" class="anchor-section" aria-label="Anchor link to header"></a></h2>
</div>
<div id="agenda" class="section level2 hasAnchor" number="1.3">
<h2 class="hasAnchor"><span class="header-section-number">1.3</span> Agenda<a href="#agenda" class="anchor-section" aria-label="Anchor link to header"></a></h2>
</div>
<div id="connecting-to-the-linux-server" class="section level2 hasAnchor" number="1.4">
<h2 class="hasAnchor"><span class="header-section-number">1.4</span> Connecting to the linux server<a href="#connecting-to-the-linux-server" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<!--chapter:end:index.Rmd-->
</div>
</div>
<div id="linux-basics" class="section level1 hasAnchor" number="2">
<h1 class="hasAnchor"><span class="header-section-number">2</span> Linux Basics<a href="#linux-basics" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<p>Placeholder</p>
<div id="connecting-to-the-linux-server-1" class="section level2 hasAnchor" number="2.1">
<h2 class="hasAnchor"><span class="header-section-number">2.1</span> Connecting to the linux server<a href="#connecting-to-the-linux-server-1" class="anchor-section" aria-label="Anchor link to header"></a></h2>
</div>
<div id="what-are-linux-bash-and-the-ncgr-server" class="section level2 hasAnchor" number="2.2">
<h2 class="hasAnchor"><span class="header-section-number">2.2</span> What are Linux, bash, and the NCGR Server?<a href="#what-are-linux-bash-and-the-ncgr-server" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="a-little-shell-aka-the-prompt-is-the-command-line-interface" class="section level3 unnumbered hasAnchor">
<h3 class="unnumbered hasAnchor">A little shell… aka the $ prompt is the command line interface<a href="#a-little-shell-aka-the-prompt-is-the-command-line-interface" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="directory-structure" class="section level3 unnumbered hasAnchor">
<h3 class="unnumbered hasAnchor">Directory Structure<a href="#directory-structure" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="find-the-shell-in-system-youll-use-to-log-into-the-ncgrs-server" class="section level3 hasAnchor" number="2.2.1">
<h3 class="hasAnchor"><span class="header-section-number">2.2.1</span> Find the shell in system you’ll use to log into the NCGR’s server<a href="#find-the-shell-in-system-youll-use-to-log-into-the-ncgrs-server" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="log-on-to-ncgrs-server" class="section level3 hasAnchor" number="2.2.2">
<h3 class="hasAnchor"><span class="header-section-number">2.2.2</span> Log on to NCGR’s server<a href="#log-on-to-ncgrs-server" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="now-that-i-logged-on-where-am-i" class="section level3 hasAnchor" number="2.2.3">
<h3 class="hasAnchor"><span class="header-section-number">2.2.3</span> Now that I logged on, where am I?<a href="#now-that-i-logged-on-where-am-i" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
</div>
<div id="linux-basics-part-i" class="section level2 hasAnchor" number="2.3">
<h2 class="hasAnchor"><span class="header-section-number">2.3</span> Linux basics: Part I:<a href="#linux-basics-part-i" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="understanding-directories" class="section level3 hasAnchor" number="2.3.1">
<h3 class="hasAnchor"><span class="header-section-number">2.3.1</span> Understanding Directories<a href="#understanding-directories" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="listing-options" class="section level3 hasAnchor" number="2.3.2">
<h3 class="hasAnchor"><span class="header-section-number">2.3.2</span> Listing options<a href="#listing-options" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="navigation" class="section level3 hasAnchor" number="2.3.3">
<h3 class="hasAnchor"><span class="header-section-number">2.3.3</span> Navigation<a href="#navigation" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="files-creating-with-touch-command" class="section level3 hasAnchor" number="2.3.4">
<h3 class="hasAnchor"><span class="header-section-number">2.3.4</span> Files: creating with touch command<a href="#files-creating-with-touch-command" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="history-command" class="section level3 hasAnchor" number="2.3.5">
<h3 class="hasAnchor"><span class="header-section-number">2.3.5</span> History command<a href="#history-command" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="files-creating-by-redirecting-standard-out" class="section level3 hasAnchor" number="2.3.6">
<h3 class="hasAnchor"><span class="header-section-number">2.3.6</span> Files: creating by redirecting standard out<a href="#files-creating-by-redirecting-standard-out" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="file-name-completion-with-tab" class="section level3 hasAnchor" number="2.3.7">
<h3 class="hasAnchor"><span class="header-section-number">2.3.7</span> File name completion with tab<a href="#file-name-completion-with-tab" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="files-moving-files-from-one-filename-to-another" class="section level3 hasAnchor" number="2.3.8">
<h3 class="hasAnchor"><span class="header-section-number">2.3.8</span> Files: moving files from one filename to another<a href="#files-moving-files-from-one-filename-to-another" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="syntax-mv-sourcefilename-destinationfilename" class="section level4 unnumbered hasAnchor">
<h4 class="unnumbered hasAnchor">Syntax: mv sourcefilename destinationfilename<a href="#syntax-mv-sourcefilename-destinationfilename" class="anchor-section" aria-label="Anchor link to header"></a></h4>
</div>
</div>
<div id="files-copying-files-from-one-filename-to-another" class="section level3 hasAnchor" number="2.3.9">
<h3 class="hasAnchor"><span class="header-section-number">2.3.9</span> Files: copying files from one filename to another<a href="#files-copying-files-from-one-filename-to-another" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="syntax-cp-sourcefilename-destinationfilename" class="section level4 unnumbered hasAnchor">
<h4 class="unnumbered hasAnchor">Syntax: cp sourcefilename destinationfilename<a href="#syntax-cp-sourcefilename-destinationfilename" class="anchor-section" aria-label="Anchor link to header"></a></h4>
</div>
</div>
<div id="files-securely-copying-files-between-your-laptop-and-ncgrs-server" class="section level3 hasAnchor" number="2.3.10">
<h3 class="hasAnchor"><span class="header-section-number">2.3.10</span> Files: securely copying files between your laptop and NCGRs server<a href="#files-securely-copying-files-between-your-laptop-and-ncgrs-server" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="syntax-scp-options-sourcepath-destinationpath" class="section level4 unnumbered hasAnchor">
<h4 class="unnumbered hasAnchor">Syntax: scp [options] sourcepath destinationpath<a href="#syntax-scp-options-sourcepath-destinationpath" class="anchor-section" aria-label="Anchor link to header"></a></h4>
</div>
</div>
<div id="files-and-directories-removing-files-is-deleting-files" class="section level3 hasAnchor" number="2.3.11">
<h3 class="hasAnchor"><span class="header-section-number">2.3.11</span> Files and directories: removing files is deleting files<a href="#files-and-directories-removing-files-is-deleting-files" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="syntax-rm-options-filename" class="section level4 unnumbered hasAnchor">
<h4 class="unnumbered hasAnchor">Syntax: rm [options] filename<a href="#syntax-rm-options-filename" class="anchor-section" aria-label="Anchor link to header"></a></h4>
</div>
</div>
<div id="tool-box-how-to-abort-a-commandprocess" class="section level3 hasAnchor" number="2.3.12">
<h3 class="hasAnchor"><span class="header-section-number">2.3.12</span> Tool box: How to abort a command/process<a href="#tool-box-how-to-abort-a-commandprocess" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
</div>
<div id="linux-basics-part-ii" class="section level2 hasAnchor" number="2.4">
<h2 class="hasAnchor"><span class="header-section-number">2.4</span> Linux basics: Part II<a href="#linux-basics-part-ii" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="files-symbolic-links-and-the-soft-link--s" class="section level3 hasAnchor" number="2.4.1">
<h3 class="hasAnchor"><span class="header-section-number">2.4.1</span> Files: Symbolic links and the soft link (-s)<a href="#files-symbolic-links-and-the-soft-link--s" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="syntax-ln--s-fileyouwanttolinkpointto-nameyouwanttogiveit" class="section level4 unnumbered hasAnchor">
<h4 class="unnumbered hasAnchor">Syntax: ln -s FileYouWantToLink/PointTo NameYouWantToGiveIt<a href="#syntax-ln--s-fileyouwanttolinkpointto-nameyouwanttogiveit" class="anchor-section" aria-label="Anchor link to header"></a></h4>
</div>
</div>
<div id="understanding-a-fasta-file-format" class="section level3 hasAnchor" number="2.4.2">
<h3 class="hasAnchor"><span class="header-section-number">2.4.2</span> Understanding a fasta file format<a href="#understanding-a-fasta-file-format" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="the-pipe-operator-will-redirect-output-of-a-command-to-another-command." class="section level4 unnumbered hasAnchor">
<h4 class="unnumbered hasAnchor">The pipe operator will redirect output of a command to another command.<a href="#the-pipe-operator-will-redirect-output-of-a-command-to-another-command." class="anchor-section" aria-label="Anchor link to header"></a></h4>
</div>
</div>
<div id="understanding-fastq-fq-file-format" class="section level3 hasAnchor" number="2.4.3">
<h3 class="hasAnchor"><span class="header-section-number">2.4.3</span> Understanding fastq (fq) file format<a href="#understanding-fastq-fq-file-format" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="what-is-the-difference-between-this-and-a-fasta-file" class="section level5 unnumbered hasAnchor">
<h5 class="unnumbered hasAnchor">What is the difference between this and a fasta file?<a href="#what-is-the-difference-between-this-and-a-fasta-file" class="anchor-section" aria-label="Anchor link to header"></a></h5>
</div>
</div>
<div id="using-grep-global-regular-expression-print-to-extract-metrics" class="section level3 hasAnchor" number="2.4.4">
<h3 class="hasAnchor"><span class="header-section-number">2.4.4</span> Using grep (global regular expression print) to extract metrics<a href="#using-grep-global-regular-expression-print-to-extract-metrics" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="syntax-grep-options-expression-filename" class="section level4 unnumbered hasAnchor">
<h4 class="unnumbered hasAnchor">Syntax: grep [options] “expression” filename<a href="#syntax-grep-options-expression-filename" class="anchor-section" aria-label="Anchor link to header"></a></h4>
</div>
</div>
<div id="working-with-compressed-files" class="section level3 hasAnchor" number="2.4.5">
<h3 class="hasAnchor"><span class="header-section-number">2.4.5</span> Working with compressed files<a href="#working-with-compressed-files" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="start-and-end-symbols" class="section level3 hasAnchor" number="2.4.6">
<h3 class="hasAnchor"><span class="header-section-number">2.4.6</span> Start ^ and end $ symbols<a href="#start-and-end-symbols" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="files-parsing-and-creating-data-subsets" class="section level3 hasAnchor" number="2.4.7">
<h3 class="hasAnchor"><span class="header-section-number">2.4.7</span> Files: parsing and creating data-subsets<a href="#files-parsing-and-creating-data-subsets" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="exercise" class="section level4 unnumbered hasAnchor">
<h4 class="unnumbered hasAnchor">Exercise:<a href="#exercise" class="anchor-section" aria-label="Anchor link to header"></a></h4>
</div>
</div>
<div id="files-parsing-and-creating-data-subsets-1" class="section level3 hasAnchor" number="2.4.8">
<h3 class="hasAnchor"><span class="header-section-number">2.4.8</span> Files: parsing and creating data-subsets<a href="#files-parsing-and-creating-data-subsets-1" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="files-parsing-and-creating-data-subsets-2" class="section level3 hasAnchor" number="2.4.9">
<h3 class="hasAnchor"><span class="header-section-number">2.4.9</span> Files: parsing and creating data-subsets<a href="#files-parsing-and-creating-data-subsets-2" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="files-parsing-and-creating-data-subsets-3" class="section level3 hasAnchor" number="2.4.10">
<h3 class="hasAnchor"><span class="header-section-number">2.4.10</span> Files: parsing and creating data-subsets<a href="#files-parsing-and-creating-data-subsets-3" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="revisiting-table1-and-previous-awk-command" class="section level3 hasAnchor" number="2.4.11">
<h3 class="hasAnchor"><span class="header-section-number">2.4.11</span> Revisiting table1 and <em>previous</em> awk command<a href="#revisiting-table1-and-previous-awk-command" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="files-stream-editor-sed" class="section level3 hasAnchor" number="2.4.12">
<h3 class="hasAnchor"><span class="header-section-number">2.4.12</span> Files: <strong>S</strong>tream <strong>ED</strong>itor (sed)<a href="#files-stream-editor-sed" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="syntax-sed-spatternreplacement" class="section level4 unnumbered hasAnchor">
<h4 class="unnumbered hasAnchor">Syntax: sed s/pattern/replacement<a href="#syntax-sed-spatternreplacement" class="anchor-section" aria-label="Anchor link to header"></a></h4>
</div>
</div>
<div id="the-bash-for-loop" class="section level3 hasAnchor" number="2.4.13">
<h3 class="hasAnchor"><span class="header-section-number">2.4.13</span> The Bash “for” Loop<a href="#the-bash-for-loop" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<div id="syntax-for-variablename-in-filenameexpression-do-command-variablename-done" class="section level4 unnumbered hasAnchor">
<h4 class="unnumbered hasAnchor">Syntax: for variablename in filenameexpression; do command ${variablename}; done<a href="#syntax-for-variablename-in-filenameexpression-do-command-variablename-done" class="anchor-section" aria-label="Anchor link to header"></a></h4>
</div>
</div>
<div id="help-with-command-syntax" class="section level3 hasAnchor" number="2.4.14">
<h3 class="hasAnchor"><span class="header-section-number">2.4.14</span> Help with command syntax<a href="#help-with-command-syntax" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="exercises" class="section level3 hasAnchor" number="2.4.15">
<h3 class="hasAnchor"><span class="header-section-number">2.4.15</span> Exercises<a href="#exercises" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
</div>
<div id="linux-basics-part-iii" class="section level2 hasAnchor" number="2.5">
<h2 class="hasAnchor"><span class="header-section-number">2.5</span> Linux basics: Part III<a href="#linux-basics-part-iii" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="using-the-screen-command" class="section level3 unnumbered hasAnchor">
<h3 class="unnumbered hasAnchor">Using the Screen Command<a href="#using-the-screen-command" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="exercise-1" class="section level3 unnumbered hasAnchor">
<h3 class="unnumbered hasAnchor">Exercise<a href="#exercise-1" class="anchor-section" aria-label="Anchor link to header"></a></h3>
</div>
<div id="more-exercises" class="section level3 hasAnchor" number="2.5.1">
<h3 class="hasAnchor"><span class="header-section-number">2.5.1</span> More Exercises<a href="#more-exercises" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<!--chapter:end:02-Linux.Rmd-->
</div>
</div>
</div>
<div id="sequence-metrics-and-quality-control" class="section level1 hasAnchor" number="3">
<h1 class="hasAnchor"><span class="header-section-number">3</span> Sequence metrics and quality Control<a href="#sequence-metrics-and-quality-control" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<div id="the-study-design" class="section level2 hasAnchor" number="3.1">
<h2 class="hasAnchor"><span class="header-section-number">3.1</span> The Study Design<a href="#the-study-design" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p><strong>3 replicates</strong> of control mice and <strong>3 replicates</strong> of water avoidance stress induced mice.<br />
We will run our own analysis on these publically-available data and compare the Differential Gene Expression and Pathway Enrichment results to those published here:<br />
<a href="https://www.mdpi.com/2218-1989/13/3/453" class="uri">https://www.mdpi.com/2218-1989/13/3/453</a></p>
<p>Why have a control?</p>
<p>Why have replicates?</p>
</div>
<div id="data-access" class="section level2 hasAnchor" number="3.2">
<h2 class="hasAnchor"><span class="header-section-number">3.2</span> Data Access<a href="#data-access" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Start a screen</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="ex">screen</span> <span class="at">-S</span> DGE</span></code></pre></div>
<p>Make a new directory branch (~/DGE_workshop/<strong>reads</strong>)</p>
<p>Enter your new directory</p>
<p>Option 1 - From your home directory:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="bu">cd</span> DGE_workshop</span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a></span>
<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a><span class="fu">mkdir</span> reads</span>
<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a></span>
<span id="cb2-5"><a href="#cb2-5" tabindex="-1"></a><span class="bu">cd</span> reads</span></code></pre></div>
<p>We have a list of 6 Sequencing Run Result (<strong>SRR</strong>) unique identifiers for samples stored in the Sequence Read Archive (SRA) database managed by NCBI. We can use this simple list (in .txt format) to download the sequences that correspond to each of the 6 SRR identifiers in the list.
Though we only have 6 samples, the sequencing <strong>depth</strong> is very high, making the download time ~ 1hr.</p>
<p><span style="color:red">Time will not allow for us to complete this command, so we will cancel the command after checking it works.</span></p>
<p>Download fastq sequence files from NCBI’s SRA:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="ex">conda</span> activate sra-tools</span>
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a></span>
<span id="cb3-3"><a href="#cb3-3" tabindex="-1"></a><span class="cf">for</span> i <span class="kw">in</span> <span class="kw">`</span><span class="fu">cat</span> SRRlist.txt<span class="kw">`;</span> <span class="cf">do</span></span>
<span id="cb3-4"><a href="#cb3-4" tabindex="-1"></a> <span class="ex">fasterq-dump</span> <span class="at">--outdir</span> . <span class="va">${line}</span></span>
<span id="cb3-5"><a href="#cb3-5" tabindex="-1"></a><span class="cf">done</span> <span class="op"><</span> ~/DGE_workshop/reads/SRRlist.txt</span></code></pre></div>
<p>Softlink the data (after you cancel the command above):</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="fu">ln</span> <span class="at">-s</span> ~/DGE_workshop/reads/<span class="pp">*</span>.gz .</span></code></pre></div>
</div>
<div id="fastp-quality-control" class="section level2 hasAnchor" number="3.3">
<h2 class="hasAnchor"><span class="header-section-number">3.3</span> fastp Quality Control<a href="#fastp-quality-control" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>It will take ~ 15 minutes to run <strong>fastp</strong> on the .fastq sequencing files for all 6 samples using 10 threads.</p>
<p>Activate the fastp environment:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="ex">conda</span> deactivate</span>
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a></span>
<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="ex">conda</span> activate fastp</span></code></pre></div>
<div class="sourceCode" id="cb6"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="cf">for</span> file <span class="kw">in</span> SRR<span class="pp">*</span><span class="kw">;</span> <span class="cf">do</span></span>
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a> <span class="va">bn</span><span class="op">=</span><span class="kw">`</span><span class="fu">basename</span> <span class="va">${file}</span> .fastq.gz<span class="kw">`</span></span>
<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a> <span class="bu">echo</span> <span class="va">$bn</span></span>
<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="cf">done</span></span></code></pre></div>
<pre><code>## SRR*</code></pre>
<p>Check the quality of our 6 sample sequences using <strong>fastp</strong>:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a></span>
<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a><span class="cf">for</span> file <span class="kw">in</span> SRR<span class="pp">*</span><span class="kw">;</span> <span class="cf">do</span></span>
<span id="cb8-3"><a href="#cb8-3" tabindex="-1"></a> <span class="va">bn</span><span class="op">=</span><span class="kw">`</span><span class="fu">basename</span> <span class="va">${file}</span> .fastq.gz<span class="kw">`</span></span>
<span id="cb8-4"><a href="#cb8-4" tabindex="-1"></a> <span class="ex">fastp</span> <span class="at">-w</span> 10 <span class="at">-h</span> <span class="st">"</span><span class="va">${file}</span><span class="st">.html"</span> <span class="at">-i</span> <span class="st">"</span><span class="va">${file}</span><span class="st">"</span> <span class="at">-o</span> <span class="st">"</span><span class="va">${bn}</span><span class="st">.fastp.fastq.gz"</span></span>
<span id="cb8-5"><a href="#cb8-5" tabindex="-1"></a><span class="cf">done</span></span></code></pre></div>
<p>Download and view the .html report.</p>
</div>
<div id="checking-sequence-metrics" class="section level2 hasAnchor" number="3.4">
<h2 class="hasAnchor"><span class="header-section-number">3.4</span> Checking Sequence Metrics<a href="#checking-sequence-metrics" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>awk “NR” variable:<br />
There are several built-in awk variables. One of them is “NR” (Number of Rows/Records). It contains line number and can be used to determine the total number of lines in a file.<br />
The following example illustrates one use of this built-in variable.</p>
<p>Prints the line number of the first 10 lines</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a><span class="fu">zcat</span> SRR23869771.fastp.fastq.gz <span class="kw">|</span> <span class="fu">awk</span> <span class="st">'{print NR}'</span> <span class="kw">|</span> <span class="fu">head</span></span></code></pre></div>
<p>awk modulo arithmatic:<br />
The modulo operator, “%”, returns the remainder of division.<br />
The expression “5 % 2”, for example, would evaluate to 1, while “9 % 3” would evaluate to 0 because the dividend (9) is a multiple of the divisor (3).</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a></span>
<span id="cb10-2"><a href="#cb10-2" tabindex="-1"></a><span class="fu">zcat</span> SRR23869771.fastp.fastq.gz <span class="kw">|</span> <span class="fu">awk</span> <span class="st">'{ if ( NR % 4 == 2) print length ($1)}'</span> <span class="kw">|</span> <span class="fu">head</span></span>
<span id="cb10-3"><a href="#cb10-3" tabindex="-1"></a></span>
<span id="cb10-4"><a href="#cb10-4" tabindex="-1"></a><span class="fu">zcat</span> SRR23869771.fastp.fastq.gz <span class="kw">|</span> <span class="fu">awk</span> <span class="st">'{ if ( NR % 4 == 2) print $0}'</span> <span class="kw">|</span> <span class="fu">wc</span> <span class="at">-l</span></span></code></pre></div>
<p>Option 2 - <span style="color:green">Advanced.</span></p>
<div class="sourceCode" id="cb11"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" tabindex="-1"></a><span class="fu">mkdir</span> <span class="at">-p</span> DGE_workshop/reads</span>
<span id="cb11-2"><a href="#cb11-2" tabindex="-1"></a></span>
<span id="cb11-3"><a href="#cb11-3" tabindex="-1"></a><span class="bu">cd</span> DGE_workshop/reads</span>
<span id="cb11-4"><a href="#cb11-4" tabindex="-1"></a></span>
<span id="cb11-5"><a href="#cb11-5" tabindex="-1"></a></span>
<span id="cb11-6"><a href="#cb11-6" tabindex="-1"></a><span class="op"><</span>!--chapter:end:03-QC.Rmd--<span class="op">></span></span>
<span id="cb11-7"><a href="#cb11-7" tabindex="-1"></a></span>
<span id="cb11-8"><a href="#cb11-8" tabindex="-1"></a></span>
<span id="cb11-9"><a href="#cb11-9" tabindex="-1"></a><span class="co"># Read Alignment</span></span>
<span id="cb11-10"><a href="#cb11-10" tabindex="-1"></a></span>
<span id="cb11-11"><a href="#cb11-11" tabindex="-1"></a><span class="ex">Placeholder</span></span>
<span id="cb11-12"><a href="#cb11-12" tabindex="-1"></a></span>
<span id="cb11-13"><a href="#cb11-13" tabindex="-1"></a></span>
<span id="cb11-14"><a href="#cb11-14" tabindex="-1"></a><span class="co">## Reference acquisition</span></span>
<span id="cb11-15"><a href="#cb11-15" tabindex="-1"></a><span class="co">## HISAT2</span></span>
<span id="cb11-16"><a href="#cb11-16" tabindex="-1"></a><span class="co">## .sam format</span></span>
<span id="cb11-17"><a href="#cb11-17" tabindex="-1"></a><span class="co">## Cigar string</span></span>
<span id="cb11-18"><a href="#cb11-18" tabindex="-1"></a><span class="co">## Alignment metrics</span></span>
<span id="cb11-19"><a href="#cb11-19" tabindex="-1"></a><span class="co">## .sam/.bam conversion and alignment sorting</span></span>
<span id="cb11-20"><a href="#cb11-20" tabindex="-1"></a></span>
<span id="cb11-21"><a href="#cb11-21" tabindex="-1"></a><span class="op"><</span>!--chapter:end:04-Alignment.Rmd--<span class="op">></span></span>
<span id="cb11-22"><a href="#cb11-22" tabindex="-1"></a></span>
<span id="cb11-23"><a href="#cb11-23" tabindex="-1"></a></span>
<span id="cb11-24"><a href="#cb11-24" tabindex="-1"></a><span class="co"># Abundance Estimation</span></span>
<span id="cb11-25"><a href="#cb11-25" tabindex="-1"></a></span>
<span id="cb11-26"><a href="#cb11-26" tabindex="-1"></a><span class="ex">Placeholder</span></span>
<span id="cb11-27"><a href="#cb11-27" tabindex="-1"></a></span>
<span id="cb11-28"><a href="#cb11-28" tabindex="-1"></a></span>
<span id="cb11-29"><a href="#cb11-29" tabindex="-1"></a><span class="co">## Format check</span></span>
<span id="cb11-30"><a href="#cb11-30" tabindex="-1"></a><span class="co">## FeatureCounts</span></span>
<span id="cb11-31"><a href="#cb11-31" tabindex="-1"></a><span class="co">### Generate counts from the alignments directory {-}</span></span>
<span id="cb11-32"><a href="#cb11-32" tabindex="-1"></a></span>
<span id="cb11-33"><a href="#cb11-33" tabindex="-1"></a><span class="op"><</span>!--chapter:end:05-Abundancy_Estimation.Rmd--<span class="op">></span></span>
<span id="cb11-34"><a href="#cb11-34" tabindex="-1"></a></span>
<span id="cb11-35"><a href="#cb11-35" tabindex="-1"></a></span>
<span id="cb11-36"><a href="#cb11-36" tabindex="-1"></a><span class="co"># Differential Gene Expression Analysis</span></span>
<span id="cb11-37"><a href="#cb11-37" tabindex="-1"></a></span>
<span id="cb11-38"><a href="#cb11-38" tabindex="-1"></a><span class="ex">Placeholder</span></span>
<span id="cb11-39"><a href="#cb11-39" tabindex="-1"></a></span>
<span id="cb11-40"><a href="#cb11-40" tabindex="-1"></a></span>
<span id="cb11-41"><a href="#cb11-41" tabindex="-1"></a><span class="co">## R data import</span></span>
<span id="cb11-42"><a href="#cb11-42" tabindex="-1"></a><span class="co">## Format metadata</span></span>
<span id="cb11-43"><a href="#cb11-43" tabindex="-1"></a><span class="co">## Normalization</span></span>
<span id="cb11-44"><a href="#cb11-44" tabindex="-1"></a><span class="co">## DESeq2</span></span>
<span id="cb11-45"><a href="#cb11-45" tabindex="-1"></a><span class="co">## Heatmap</span></span>
<span id="cb11-46"><a href="#cb11-46" tabindex="-1"></a><span class="co">## Gene count plots</span></span>
<span id="cb11-47"><a href="#cb11-47" tabindex="-1"></a></span>
<span id="cb11-48"><a href="#cb11-48" tabindex="-1"></a><span class="op"><</span>!--chapter:end:06-DGE.Rmd--<span class="op">></span></span>
<span id="cb11-49"><a href="#cb11-49" tabindex="-1"></a></span>
<span id="cb11-50"><a href="#cb11-50" tabindex="-1"></a></span>
<span id="cb11-51"><a href="#cb11-51" tabindex="-1"></a><span class="co"># Additional visualization</span></span>
<span id="cb11-52"><a href="#cb11-52" tabindex="-1"></a></span>
<span id="cb11-53"><a href="#cb11-53" tabindex="-1"></a><span class="ex">Placeholder</span></span>
<span id="cb11-54"><a href="#cb11-54" tabindex="-1"></a></span>
<span id="cb11-55"><a href="#cb11-55" tabindex="-1"></a></span>
<span id="cb11-56"><a href="#cb11-56" tabindex="-1"></a><span class="co">## Graphing with ggplot2</span></span>
<span id="cb11-57"><a href="#cb11-57" tabindex="-1"></a><span class="co">## Data and setup</span></span>
<span id="cb11-58"><a href="#cb11-58" tabindex="-1"></a><span class="co">## Scatter plots</span></span>
<span id="cb11-59"><a href="#cb11-59" tabindex="-1"></a><span class="co">## Volcano plot</span></span>
<span id="cb11-60"><a href="#cb11-60" tabindex="-1"></a><span class="co">## Boxplots</span></span>
<span id="cb11-61"><a href="#cb11-61" tabindex="-1"></a><span class="co">## Violin plots</span></span>
<span id="cb11-62"><a href="#cb11-62" tabindex="-1"></a><span class="co">## Interactive Plots</span></span>
<span id="cb11-63"><a href="#cb11-63" tabindex="-1"></a><span class="co">## Homework (optional)</span></span>
<span id="cb11-64"><a href="#cb11-64" tabindex="-1"></a></span>
<span id="cb11-65"><a href="#cb11-65" tabindex="-1"></a><span class="op"><</span>!--chapter:end:07-Additional_Visualization.Rmd--<span class="op">></span></span>
<span id="cb11-66"><a href="#cb11-66" tabindex="-1"></a></span>
<span id="cb11-67"><a href="#cb11-67" tabindex="-1"></a></span>
<span id="cb11-68"><a href="#cb11-68" tabindex="-1"></a><span class="co"># Pathway Enrichment Analysis</span></span>
<span id="cb11-69"><a href="#cb11-69" tabindex="-1"></a></span>
<span id="cb11-70"><a href="#cb11-70" tabindex="-1"></a><span class="ex">Placeholder</span></span>
<span id="cb11-71"><a href="#cb11-71" tabindex="-1"></a></span>
<span id="cb11-72"><a href="#cb11-72" tabindex="-1"></a></span>
<span id="cb11-73"><a href="#cb11-73" tabindex="-1"></a><span class="co">## Parsing</span></span>
<span id="cb11-74"><a href="#cb11-74" tabindex="-1"></a><span class="co">## Cytoscape and ClueGO</span></span>
<span id="cb11-75"><a href="#cb11-75" tabindex="-1"></a><span class="co">## Additional options</span></span>
<span id="cb11-76"><a href="#cb11-76" tabindex="-1"></a><span class="co">## CluePedia</span></span>
<span id="cb11-77"><a href="#cb11-77" tabindex="-1"></a></span>
<span id="cb11-78"><a href="#cb11-78" tabindex="-1"></a><span class="op"><</span>!--chapter:end:08-PE.Rmd--<span class="op">></span></span>
<span id="cb11-79"><a href="#cb11-79" tabindex="-1"></a></span>
<span id="cb11-80"><a href="#cb11-80" tabindex="-1"></a></span>
<span id="cb11-81"><a href="#cb11-81" tabindex="-1"></a><span class="co"># Coexpression Networks</span></span>
<span id="cb11-82"><a href="#cb11-82" tabindex="-1"></a></span>
<span id="cb11-83"><a href="#cb11-83" tabindex="-1"></a><span class="ex">Placeholder</span></span>
<span id="cb11-84"><a href="#cb11-84" tabindex="-1"></a></span>
<span id="cb11-85"><a href="#cb11-85" tabindex="-1"></a></span>
<span id="cb11-86"><a href="#cb11-86" tabindex="-1"></a><span class="co">## Preparing the environment</span></span>
<span id="cb11-87"><a href="#cb11-87" tabindex="-1"></a><span class="co">## Read in data</span></span>
<span id="cb11-88"><a href="#cb11-88" tabindex="-1"></a><span class="co">## Check Samples and Genes</span></span>
<span id="cb11-89"><a href="#cb11-89" tabindex="-1"></a><span class="co">## Sample outliers</span></span>
<span id="cb11-90"><a href="#cb11-90" tabindex="-1"></a><span class="co">## Get the phenotype data</span></span>
<span id="cb11-91"><a href="#cb11-91" tabindex="-1"></a><span class="co">## Filter and normalize genes </span></span>
<span id="cb11-92"><a href="#cb11-92" tabindex="-1"></a><span class="co">## Soft-threshold</span></span>
<span id="cb11-93"><a href="#cb11-93" tabindex="-1"></a><span class="co">## Create Network</span></span>
<span id="cb11-94"><a href="#cb11-94" tabindex="-1"></a><span class="co">## Get the module eigengenes</span></span>
<span id="cb11-95"><a href="#cb11-95" tabindex="-1"></a><span class="co">## Compare modules to phenotypes</span></span>
<span id="cb11-96"><a href="#cb11-96" tabindex="-1"></a><span class="co">## Driver genes</span></span>
<span id="cb11-97"><a href="#cb11-97" tabindex="-1"></a></span>
<span id="cb11-98"><a href="#cb11-98" tabindex="-1"></a><span class="op"><</span>!--chapter:end:09-CoexpressionNetworks.Rmd--<span class="op">></span></span>
<span id="cb11-99"><a href="#cb11-99" tabindex="-1"></a></span>
<span id="cb11-100"><a href="#cb11-100" tabindex="-1"></a></span>
<span id="cb11-101"><a href="#cb11-101" tabindex="-1"></a><span class="co"># Sequencing Technologies and Lab Protocols</span></span>
<span id="cb11-102"><a href="#cb11-102" tabindex="-1"></a></span>
<span id="cb11-103"><a href="#cb11-103" tabindex="-1"></a><span class="ex">Placeholder</span></span>
<span id="cb11-104"><a href="#cb11-104" tabindex="-1"></a></span>
<span id="cb11-105"><a href="#cb11-105" tabindex="-1"></a></span>
<span id="cb11-106"><a href="#cb11-106" tabindex="-1"></a><span class="co">## Sequencing technologies</span></span>
<span id="cb11-107"><a href="#cb11-107" tabindex="-1"></a><span class="co">#### Short Reads{-}</span></span>
<span id="cb11-108"><a href="#cb11-108" tabindex="-1"></a><span class="co">#### Long Reads{-}</span></span>
<span id="cb11-109"><a href="#cb11-109" tabindex="-1"></a><span class="co">### Sanger Sequencing</span></span>
<span id="cb11-110"><a href="#cb11-110" tabindex="-1"></a><span class="co">## Illumina Sequencing</span></span>
<span id="cb11-111"><a href="#cb11-111" tabindex="-1"></a><span class="co">## PacBio Sequencing</span></span>
<span id="cb11-112"><a href="#cb11-112" tabindex="-1"></a><span class="co">## Oxford Nanopore Sequencing</span></span>
<span id="cb11-113"><a href="#cb11-113" tabindex="-1"></a></span>
<span id="cb11-114"><a href="#cb11-114" tabindex="-1"></a><span class="op"><</span>!--chapter:end:10-SeqTechLabProtocols.Rmd--<span class="op">></span></span>
<span id="cb11-115"><a href="#cb11-115" tabindex="-1"></a></span>
<span id="cb11-116"><a href="#cb11-116" tabindex="-1"></a></span>
<span id="cb11-117"><a href="#cb11-117" tabindex="-1"></a><span class="co"># DESeq2 Model Design</span></span>
<span id="cb11-118"><a href="#cb11-118" tabindex="-1"></a></span>
<span id="cb11-119"><a href="#cb11-119" tabindex="-1"></a><span class="ex">Placeholder</span></span>
<span id="cb11-120"><a href="#cb11-120" tabindex="-1"></a></span>
<span id="cb11-121"><a href="#cb11-121" tabindex="-1"></a></span>
<span id="cb11-122"><a href="#cb11-122" tabindex="-1"></a><span class="co">## One Factor</span></span>
<span id="cb11-123"><a href="#cb11-123" tabindex="-1"></a><span class="co">## Two Factors</span></span>
<span id="cb11-124"><a href="#cb11-124" tabindex="-1"></a><span class="co">## A little bit on statistical tests</span></span>
<span id="cb11-125"><a href="#cb11-125" tabindex="-1"></a><span class="co">## Time series</span></span>
<span id="cb11-126"><a href="#cb11-126" tabindex="-1"></a><span class="co">## More resources</span></span>
<span id="cb11-127"><a href="#cb11-127" tabindex="-1"></a></span>
<span id="cb11-128"><a href="#cb11-128" tabindex="-1"></a><span class="op"><</span>!--chapter:end:11-ModelsStatistics.Rmd--<span class="op">></span></span>
<span id="cb11-129"><a href="#cb11-129" tabindex="-1"></a></span>
<span id="cb11-130"><a href="#cb11-130" tabindex="-1"></a></span>
<span id="cb11-131"><a href="#cb11-131" tabindex="-1"></a><span class="co"># Wrap Up</span></span>
<span id="cb11-132"><a href="#cb11-132" tabindex="-1"></a></span>
<span id="cb11-133"><a href="#cb11-133" tabindex="-1"></a><span class="ex">Placeholder</span></span>
<span id="cb11-134"><a href="#cb11-134" tabindex="-1"></a></span>
<span id="cb11-135"><a href="#cb11-135" tabindex="-1"></a></span>
<span id="cb11-136"><a href="#cb11-136" tabindex="-1"></a><span class="co">## Acknowledgement</span></span>
<span id="cb11-137"><a href="#cb11-137" tabindex="-1"></a><span class="co">## Survey</span></span>
<span id="cb11-138"><a href="#cb11-138" tabindex="-1"></a><span class="co">## Questions</span></span>
<span id="cb11-139"><a href="#cb11-139" tabindex="-1"></a><span class="co">## Server access and acknowledgements</span></span>
<span id="cb11-140"><a href="#cb11-140" tabindex="-1"></a><span class="co">## Bookdown document</span></span>
<span id="cb11-141"><a href="#cb11-141" tabindex="-1"></a><span class="co">## Zoom recordings</span></span>
<span id="cb11-142"><a href="#cb11-142" tabindex="-1"></a></span>
<span id="cb11-143"><a href="#cb11-143" tabindex="-1"></a><span class="op"><</span>!--chapter:end:12-WrapUp.Rmd--<span class="op">></span></span></code></pre></div>
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