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            <h1 id="seo-header">STAR：记录一次比对过程</h1>
            
            
              <div class="markdown-body">
                
                <h2 id="数据准备"><a href="#数据准备" class="headerlink" title="数据准备"></a>数据准备</h2><figure class="highlight sh"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br></pre></td><td class="code"><pre><code class="hljs sh">.<br>├── gencode.vM29.primary_assembly.annotation.gtf<br>├── GRCm39.primary_assembly.genome.fa<br>├── index<br>│   ├── chrLength.txt<br>│   ├── chrNameLength.txt<br>│   ├── chrName.txt<br>│   ├── chrStart.txt<br>│   ├── exonGeTrInfo.tab<br>│   ├── exonInfo.tab<br>│   ├── geneInfo.tab<br>│   ├── Genome<br>│   ├── genomeParameters.txt<br>│   ├── Log.out<br>│   ├── SA<br>│   ├── SAindex<br>│   ├── sjdbInfo.txt<br>│   ├── sjdbList.fromGTF.out.tab<br>│   ├── sjdbList.out.tab<br>│   └── transcriptInfo.tab<br>└── XL789vs123<br>    ├── XL1<br>    │   └── default_s.fq.gz<br>    ├── XL2<br>    │   └── default_s.fq.gz<br>    ├── XL3<br>    │   └── default_s.fq.gz<br>    ├── XL7<br>    │   └── default_s.fq.gz<br>    ├── XL8<br>    │   └── default_s.fq.gz<br>    └── XL9<br>        └── default_s.fq.gz<br></code></pre></td></tr></table></figure>

<p><a href="https://occdn.limour.top/1929.html">https://occdn.limour.top/1929.html</a></p>
<p><a href="https://occdn.limour.top/1932.html">https://occdn.limour.top/1932.html</a></p>
<ul>
<li>XL789vs123中的fasta文件可以来自公司的cleandata，也可以从bam文件生成</li>
<li>index中的文件为STAR使用参考基因组fasta文件和对应的gtf注释生成</li>
</ul>
<h2 id="第三步-第一次对比"><a href="#第三步-第一次对比" class="headerlink" title="第三步 第一次对比"></a>第三步 第一次对比</h2><figure class="highlight sh"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br><span class="line">45</span><br><span class="line">46</span><br><span class="line">47</span><br></pre></td><td class="code"><pre><code class="hljs sh"><span class="hljs-meta">#!/bin/sh</span><br><span class="hljs-comment">#设置CleanData存放目录</span><br>CLEAN=/home/jovyan/upload/22.07.02/XL789vs123<br><span class="hljs-comment">#设置输出目录</span><br>WORK=/home/jovyan/upload/22.07.02/output_XL789vs123<br><span class="hljs-comment">#设置index目录</span><br>INDEX=/home/jovyan/upload/22.07.02/index<br><span class="hljs-comment">#设置参考文件位置</span><br>Reference=/home/jovyan/upload/22.07.02/GRCm39.primary_assembly.genome.fa<br><span class="hljs-comment">#设置 sjdbOverhang</span><br>sjdbOverhang=49<br> <br><span class="hljs-built_in">echo</span> <span class="hljs-variable">$CLEAN</span><span class="hljs-string">&quot;, &quot;</span><span class="hljs-variable">$WORK</span><span class="hljs-string">&quot;, &quot;</span><span class="hljs-variable">$INDEX</span><br><span class="hljs-built_in">mkdir</span> <span class="hljs-variable">$WORK</span><br> <br>CDIR=$(<span class="hljs-built_in">basename</span> `<span class="hljs-built_in">pwd</span>`)<br><span class="hljs-built_in">echo</span> <span class="hljs-variable">$CDIR</span><br><span class="hljs-built_in">echo</span> <span class="hljs-variable">$CLEAN</span><br><span class="hljs-keyword">for</span> file <span class="hljs-keyword">in</span> <span class="hljs-variable">$CLEAN</span>/*<br><span class="hljs-keyword">do</span><br><span class="hljs-built_in">echo</span> <span class="hljs-variable">$file</span><br>SAMPLE=<span class="hljs-variable">$&#123;file##*/&#125;</span><br><span class="hljs-built_in">echo</span> <span class="hljs-variable">$SAMPLE</span><br><span class="hljs-built_in">mkdir</span> <span class="hljs-variable">$WORK</span><span class="hljs-string">&quot;/&quot;</span><span class="hljs-variable">$SAMPLE</span><br><span class="hljs-built_in">cd</span> <span class="hljs-variable">$WORK</span><span class="hljs-string">&quot;/&quot;</span><span class="hljs-variable">$SAMPLE</span><br> <br>STAR \<br>--genomeDir <span class="hljs-variable">$INDEX</span> \<br>--readFilesIn `<span class="hljs-built_in">ls</span> <span class="hljs-variable">$CLEAN</span>/<span class="hljs-variable">$SAMPLE</span>/*` \<br>--runThreadN 4 \<br>--outFilterMultimapScoreRange 1 \<br>--outFilterMultimapNmax 20 \<br>--outFilterMismatchNmax 10 \<br>--alignIntronMax 500000 \<br>--alignMatesGapMax 1000000 \<br>--sjdbScore 2 \<br>--alignSJDBoverhangMin 1 \<br>--genomeLoad LoadAndRemove \<br>--readFilesCommand zcat \<br>--outFilterMatchNminOverLread 0.33 \<br>--outFilterScoreMinOverLread 0.33 \<br>--sjdbOverhang <span class="hljs-variable">$sjdbOverhang</span> \<br>--outSAMstrandField intronMotif \<br>--outSAMtype None \<br>--outSAMmode None \<br> <br><span class="hljs-keyword">done</span><br></code></pre></td></tr></table></figure>

<ul>
<li>nano 3.sh</li>
<li>chmod +x 3.sh</li>
<li>.&#x2F;3.sh 将得到以下输出</li>
</ul>
<figure class="highlight sh"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br></pre></td><td class="code"><pre><code class="hljs sh">output_XL789vs123/<br>├── XL1<br>│   ├── Log.final.out<br>│   ├── Log.out<br>│   ├── Log.progress.out<br>│   └── SJ.out.tab<br>├── XL2<br>│   ├── Log.final.out<br>│   ├── Log.out<br>│   ├── Log.progress.out<br>│   └── SJ.out.tab<br>├── XL3<br>│   ├── Log.final.out<br>│   ├── Log.out<br>│   ├── Log.progress.out<br>│   └── SJ.out.tab<br>├── XL7<br>│   ├── Log.final.out<br>│   ├── Log.out<br>│   ├── Log.progress.out<br>│   └── SJ.out.tab<br>├── XL8<br>│   ├── Log.final.out<br>│   ├── Log.out<br>│   ├── Log.progress.out<br>│   └── SJ.out.tab<br>└── XL9<br>    ├── Log.final.out<br>    ├── Log.out<br>    ├── Log.progress.out<br>    └── SJ.out.tab<br></code></pre></td></tr></table></figure>

<h2 id="第四步-建立中间索引"><a href="#第四步-建立中间索引" class="headerlink" title="第四步 建立中间索引"></a>第四步 建立中间索引</h2><figure class="highlight sh"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br></pre></td><td class="code"><pre><code class="hljs sh"><span class="hljs-meta">#!/bin/sh</span><br><span class="hljs-comment">#设置CleanData存放目录</span><br>CLEAN=/home/jovyan/upload/22.07.02/XL789vs123<br><span class="hljs-comment">#设置第三步的输出目录(上一步的输出目录)</span><br>WORK=/home/jovyan/upload/22.07.02/output_XL789vs123<br><span class="hljs-comment">#设置index目录</span><br>INDEX=/home/jovyan/upload/22.07.02/index<br><span class="hljs-comment">#设置参考文件位置</span><br>Reference=/home/jovyan/upload/22.07.02/GRCm39.primary_assembly.genome.fa<br><span class="hljs-comment">#设置 sjdbOverhang</span><br>sjdbOverhang=49<br><span class="hljs-comment">#设置 IIG 目录(这一步的输出目录)</span><br>IIG=/home/jovyan/upload/22.07.02/IIG_XL789vs123<br><br></code></pre></td></tr></table></figure>

<ul>
<li>nano 4.sh</li>
<li>chmod +x 4.sh</li>
<li>.&#x2F;4.sh 将得到以下输出</li>
</ul>
<figure class="highlight sh"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br></pre></td><td class="code"><pre><code class="hljs sh">IIG_XL789vs123/<br>├── chrLength.txt<br>├── chrNameLength.txt<br>├── chrName.txt<br>├── chrStart.txt<br>├── Genome<br>├── genomeParameters.txt<br>├── Log.out<br>├── SA<br>├── SAindex<br>├── sjdbInfo.txt<br>└── sjdbList.out.tab<br></code></pre></td></tr></table></figure>

<h2 id="第五步-第二次对比"><a href="#第五步-第二次对比" class="headerlink" title="第五步 第二次对比"></a>第五步 第二次对比</h2><figure class="highlight sh"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br><span class="line">45</span><br><span class="line">46</span><br><span class="line">47</span><br><span class="line">48</span><br><span class="line">49</span><br><span class="line">50</span><br><span class="line">51</span><br><span class="line">52</span><br><span class="line">53</span><br><span class="line">54</span><br><span class="line">55</span><br><span class="line">56</span><br><span class="line">57</span><br></pre></td><td class="code"><pre><code class="hljs sh"><span class="hljs-meta">#!/bin/sh</span><br><span class="hljs-comment">#设置CleanData存放目录</span><br>CLEAN=/home/jovyan/upload/22.07.02/XL789vs123<br><span class="hljs-comment">#设置第三步的输出目录</span><br>WORK=/home/jovyan/upload/22.07.02/output_XL789vs123<br><span class="hljs-comment">#设置index目录</span><br>INDEX=/home/jovyan/upload/22.07.02/index<br><span class="hljs-comment">#设置参考文件位置</span><br>Reference=/home/jovyan/upload/22.07.02/GRCm39.primary_assembly.genome.fa<br><span class="hljs-comment">#设置 sjdbOverhang</span><br>sjdbOverhang=49<br><span class="hljs-comment">#设置 IIG 目录(第四步的输出目录)</span><br>IIG=/home/jovyan/upload/22.07.02/IIG_XL789vs123<br> <br><span class="hljs-built_in">ln</span> -s <span class="hljs-variable">$INDEX</span>/exonGeTrInfo.tab <span class="hljs-variable">$IIG</span><br><span class="hljs-built_in">ln</span> -s <span class="hljs-variable">$INDEX</span>/exonInfo.tab <span class="hljs-variable">$IIG</span><br><span class="hljs-built_in">ln</span> -s <span class="hljs-variable">$INDEX</span>/geneInfo.tab <span class="hljs-variable">$IIG</span><br><span class="hljs-built_in">ln</span> -s <span class="hljs-variable">$INDEX</span>/sjdbList.fromGTF.out.tab <span class="hljs-variable">$IIG</span><br><span class="hljs-built_in">ln</span> -s <span class="hljs-variable">$INDEX</span>/transcriptInfo.tab <span class="hljs-variable">$IIG</span><br> <br>CDIR=$(<span class="hljs-built_in">basename</span> `<span class="hljs-built_in">pwd</span>`)<br><span class="hljs-built_in">echo</span> <span class="hljs-variable">$CDIR</span><br><span class="hljs-built_in">echo</span> <span class="hljs-variable">$CLEAN</span><br><span class="hljs-keyword">for</span> file <span class="hljs-keyword">in</span> <span class="hljs-variable">$CLEAN</span>/*<br><span class="hljs-keyword">do</span><br><span class="hljs-built_in">echo</span> <span class="hljs-variable">$file</span><br>SAMPLE=<span class="hljs-variable">$&#123;file##*/&#125;</span><br><span class="hljs-built_in">echo</span> <span class="hljs-variable">$WORK</span><span class="hljs-string">&quot;/&quot;</span><span class="hljs-variable">$SAMPLE</span><br><span class="hljs-built_in">mkdir</span> <span class="hljs-variable">$WORK</span><span class="hljs-string">&quot;/&quot;</span><span class="hljs-variable">$SAMPLE</span><span class="hljs-string">&quot;/Res&quot;</span><br><span class="hljs-built_in">cd</span> <span class="hljs-variable">$WORK</span><span class="hljs-string">&quot;/&quot;</span><span class="hljs-variable">$SAMPLE</span><span class="hljs-string">&quot;/Res&quot;</span><br> <br>STAR \<br>--genomeDir <span class="hljs-variable">$IIG</span> \<br>--readFilesIn `<span class="hljs-built_in">ls</span> <span class="hljs-variable">$CLEAN</span>/<span class="hljs-variable">$SAMPLE</span>/*` \<br>--runThreadN 8 \<br>--quantMode TranscriptomeSAM GeneCounts \<br>--outFilterMultimapScoreRange 1 \<br>--outFilterMultimapNmax 20 \<br>--outFilterMismatchNmax 10 \<br>--alignIntronMax 500000 \<br>--alignMatesGapMax 1000000 \<br>--sjdbScore 2 \<br>--alignSJDBoverhangMin 1 \<br>--genomeLoad LoadAndRemove \<br>--limitBAMsortRAM  35000000000 \<br>--readFilesCommand zcat \<br>--outFilterMatchNminOverLread 0.33 \<br>--outFilterScoreMinOverLread 0.33 \<br>--sjdbOverhang <span class="hljs-variable">$sjdbOverhang</span> \<br>--outSAMstrandField intronMotif \<br>--outSAMattributes NH HI NM MD AS XS \<br>--outSAMunmapped Within \<br>--outSAMtype BAM SortedByCoordinate \<br>--outSAMheaderHD @HD VN:1.4 \<br>--outSAMattrRGline ID:sample SM:sample PL:ILLUMINA<br> <br><span class="hljs-keyword">done</span><br></code></pre></td></tr></table></figure>

<ul>
<li>nano 5.sh</li>
<li>chmod +x 5.sh</li>
<li>.&#x2F;5.sh 将得到以下输出</li>
</ul>
<figure class="highlight sh"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br></pre></td><td class="code"><pre><code class="hljs sh">output_XL789vs123/XL1/Res/<br>├── Aligned.sortedByCoord.out.bam<br>├── Aligned.toTranscriptome.out.bam<br>├── Log.final.out<br>├── Log.out<br>├── Log.progress.out<br>├── ReadsPerGene.out.tab<br>└── SJ.out.tab<br></code></pre></td></tr></table></figure>

<h2 id="第六步-组装Counts文件"><a href="#第六步-组装Counts文件" class="headerlink" title="第六步 组装Counts文件"></a>第六步 组装Counts文件</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment">#设置第三步的输出目录</span><br>WORK<span class="hljs-operator">=</span><span class="hljs-string">&#x27;/home/jovyan/upload/22.07.02/output_XL789vs123&#x27;</span><br><span class="hljs-comment">#设置index中基因注释位置</span><br>Reference<span class="hljs-operator">=</span><span class="hljs-string">&#x27;/home/jovyan/upload/22.07.02/index/geneInfo.tab&#x27;</span><br>file_list <span class="hljs-operator">&lt;-</span> list.dirs<span class="hljs-punctuation">(</span>WORK<span class="hljs-punctuation">,</span> recursive<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> full.names <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br>geneN <span class="hljs-operator">&lt;-</span> read.table<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> Reference<span class="hljs-punctuation">,</span> sep <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;\t&#x27;</span><span class="hljs-punctuation">,</span> skip <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>colnames<span class="hljs-punctuation">(</span>geneN<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;ID&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;symbol&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;type&#x27;</span><span class="hljs-punctuation">)</span><br><span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>sample <span class="hljs-keyword">in</span> file_list<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    test_tab <span class="hljs-operator">&lt;-</span> read.table<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> file.path<span class="hljs-punctuation">(</span>WORK<span class="hljs-punctuation">,</span> sample<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Res&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;ReadsPerGene.out.tab&#x27;</span><span class="hljs-punctuation">)</span> <span class="hljs-punctuation">,</span> sep <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;\t&#x27;</span><span class="hljs-punctuation">,</span> header <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br>    test_tab <span class="hljs-operator">&lt;-</span> test_tab<span class="hljs-punctuation">[</span><span class="hljs-operator">-</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-punctuation">]</span><br>    geneN<span class="hljs-punctuation">[</span>sample<span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> test_tab<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><br><span class="hljs-punctuation">&#125;</span><br>write.csv<span class="hljs-punctuation">(</span>x <span class="hljs-operator">=</span> geneN<span class="hljs-punctuation">,</span> file <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;XL789vs123.csv&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<p><img src="https://img-cdn.limour.top/blog/20220702142511.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></p>
<p>组装的Counts文件格式</p>
<h2 id="第七步-差异基因分析"><a href="#第七步-差异基因分析" class="headerlink" title="第七步 差异基因分析"></a>第七步 差异基因分析</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>DESeq2<span class="hljs-punctuation">)</span><br>count_all <span class="hljs-operator">&lt;-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;XL789vs123.csv&quot;</span><span class="hljs-punctuation">,</span>header<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span>row.names<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>count_all<br>cts_b <span class="hljs-operator">&lt;-</span> count_all<span class="hljs-punctuation">[</span> <span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-operator">-</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-operator">-</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>rownames<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> count_all<span class="hljs-operator">$</span>ID<br>conditions <span class="hljs-operator">&lt;-</span> factor<span class="hljs-punctuation">(</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Control&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;XL&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>    <br>colData_b <span class="hljs-operator">&lt;-</span> data.frame<span class="hljs-punctuation">(</span>row.names <span class="hljs-operator">=</span> colnames<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> conditions<span class="hljs-punctuation">)</span><br>colData_b<br>dds <span class="hljs-operator">&lt;-</span> DESeqDataSetFromMatrix<span class="hljs-punctuation">(</span>countData <span class="hljs-operator">=</span> cts_b<span class="hljs-punctuation">,</span><br>                              colData <span class="hljs-operator">=</span> colData_b<span class="hljs-punctuation">,</span><br>                              design <span class="hljs-operator">=</span> <span class="hljs-operator">~</span> conditions<span class="hljs-punctuation">)</span><br>dds <span class="hljs-operator">&lt;-</span> DESeq<span class="hljs-punctuation">(</span>dds<span class="hljs-punctuation">)</span><br>res <span class="hljs-operator">&lt;-</span> results<span class="hljs-punctuation">(</span>dds<span class="hljs-punctuation">)</span><br>rres <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>count_all<span class="hljs-punctuation">,</span> data.frame<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>write.csv<span class="hljs-punctuation">(</span>rres<span class="hljs-punctuation">,</span> file<span class="hljs-operator">=</span><span class="hljs-string">&#x27;XL789vs123_DESeq2.csv&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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