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            <h1 id="seo-header">STAR：一键脚本</h1>
            
            
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                <h2 id="可选：BAM转FASTQ"><a href="#可选：BAM转FASTQ" class="headerlink" title="可选：BAM转FASTQ"></a>可选：BAM转FASTQ</h2><p>将所有bam文件以.bam结尾，单独存放到一个目录，conda activate biobambam，新建以下脚本运行</p>
<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></pre></td><td class="code"><pre><code class="hljs sh"><span class="hljs-meta">#!/bin/sh</span><br>ROOT=/home/jovyan/upload/22.07.02/muscle<br><span class="hljs-built_in">mkdir</span> <span class="hljs-variable">$ROOT</span><br> <br><span class="hljs-keyword">for</span> _ <span class="hljs-keyword">in</span> *.bam<br><span class="hljs-keyword">do</span><br> <br><span class="hljs-built_in">mkdir</span> <span class="hljs-variable">$ROOT</span>/<span class="hljs-variable">$&#123;_%.bam&#125;</span><br> <br>bamtofastq \<br>collate=1 \<br>exclude=QCFAIL,SECONDARY,SUPPLEMENTARY \<br>filename=<span class="hljs-variable">$_</span> \<br>gz=1 \<br>inputformat=bam \<br>level=5 \<br>outputdir=<span class="hljs-variable">$ROOT</span>/<span class="hljs-variable">$&#123;_%.bam&#125;</span> \<br>outputperreadgroup=1 \<br>outputperreadgroupsuffixF=_1.fq.gz \<br>outputperreadgroupsuffixF2=_2.fq.gz \<br>outputperreadgroupsuffixO=_o1.fq.gz \<br>outputperreadgroupsuffixO2=_o2.fq.gz \<br>outputperreadgroupsuffixS=_s.fq.gz \<br>tryoq=1 \<br> <br><span class="hljs-keyword">done</span><br></code></pre></td></tr></table></figure>

<h2 id="一键脚本"><a href="#一键脚本" class="headerlink" title="一键脚本"></a>一键脚本</h2><p>单独起一个目录，在这个目录下，以样本名为目录名，将样本的fataq文件以gzip压缩后存放，单端一个文件，双端两个文件，都可以，示例结构如下</p>
<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></pre></td><td class="code"><pre><code class="hljs sh">XL1_12/<br>├── XL01<br>│   └── default_s.fq.gz<br>├── XL02<br>│   └── default_s.fq.gz<br>├── XL03<br>│   └── default_s.fq.gz<br>├── XL04<br>│   └── default_s.fq.gz<br>├── XL05<br>│   └── default_s.fq.gz<br>├── XL06<br>│   └── default_s.fq.gz<br>├── XL07<br>│   └── default_s.fq.gz<br>├── XL08<br>│   └── default_s.fq.gz<br>├── XL09<br>│   └── default_s.fq.gz<br>├── XL10<br>│   └── default_s.fq.gz<br>├── XL11<br>│   └── default_s.fq.gz<br>└── XL12<br>    └── default_s.fq.gz<br></code></pre></td></tr></table></figure>

<p>在这个目录外，conda activate star，新建以下脚本运行，即可跑完前五步</p>
<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><span class="line">58</span><br><span class="line">59</span><br><span class="line">60</span><br><span class="line">61</span><br><span class="line">62</span><br><span class="line">63</span><br><span class="line">64</span><br><span class="line">65</span><br><span class="line">66</span><br><span class="line">67</span><br><span class="line">68</span><br><span class="line">69</span><br><span class="line">70</span><br><span class="line">71</span><br><span class="line">72</span><br><span class="line">73</span><br><span class="line">74</span><br><span class="line">75</span><br><span class="line">76</span><br><span class="line">77</span><br><span class="line">78</span><br><span class="line">79</span><br><span class="line">80</span><br><span class="line">81</span><br><span class="line">82</span><br><span class="line">83</span><br><span class="line">84</span><br><span class="line">85</span><br><span class="line">86</span><br><span class="line">87</span><br><span class="line">88</span><br><span class="line">89</span><br><span class="line">90</span><br><span class="line">91</span><br><span class="line">92</span><br><span class="line">93</span><br><span class="line">94</span><br><span class="line">95</span><br><span class="line">96</span><br><span class="line">97</span><br><span class="line">98</span><br><span class="line">99</span><br><span class="line">100</span><br><span class="line">101</span><br><span class="line">102</span><br><span class="line">103</span><br><span class="line">104</span><br><span class="line">105</span><br><span class="line">106</span><br><span class="line">107</span><br><span class="line">108</span><br><span class="line">109</span><br><span class="line">110</span><br><span class="line">111</span><br><span class="line">112</span><br><span class="line">113</span><br><span class="line">114</span><br><span class="line">115</span><br><span class="line">116</span><br></pre></td><td class="code"><pre><code class="hljs sh"><span class="hljs-meta">#!/bin/sh</span><br><span class="hljs-comment">#任务名</span><br>TASKN=XL1_12<br><span class="hljs-comment">#设置CleanData存放目录</span><br>CLEAN=/home/jovyan/upload/22.07.02/<span class="hljs-variable">$TASKN</span><br><span class="hljs-comment">#设置输出目录</span><br>WORK=/home/jovyan/upload/22.07.02/output_<span class="hljs-variable">$TASKN</span><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_<span class="hljs-variable">$TASKN</span><br> <br><span class="hljs-built_in">echo</span> <span class="hljs-variable">$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> <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">$INDEX</span><span class="hljs-string">&quot;, &quot;</span><span class="hljs-variable">$IIG</span><br><span class="hljs-built_in">mkdir</span> <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">$SAMPLE</span><br><span class="hljs-keyword">done</span><br> <br>STAR \<br>--runMode genomeGenerate \<br>--genomeDir <span class="hljs-variable">$IIG</span> \<br>--genomeFastaFiles <span class="hljs-variable">$Reference</span> \<br>--sjdbOverhang <span class="hljs-variable">$sjdbOverhang</span> \<br>--runThreadN 4 \<br>--sjdbFileChrStartEnd `<span class="hljs-built_in">ls</span> <span class="hljs-variable">$WORK</span>/*/SJ.out.tab`<br> <br><span class="hljs-built_in">ln</span> -s <span class="hljs-variable">$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>

<h2 id="DESeq2分析"><a href="#DESeq2分析" class="headerlink" title="DESeq2分析"></a>DESeq2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><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></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;liver.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>cts_bb <span class="hljs-operator">&lt;-</span> cts_b<br> <br>cts_b <span class="hljs-operator">&lt;-</span> cts_bb<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-string">&#x27;XL07&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;XL08&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;XL09&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;XL10&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;XL11&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;XL12&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>keep <span class="hljs-operator">&lt;-</span> rowSums<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">)</span> <span class="hljs-operator">&gt;</span> <span class="hljs-number">10</span><br>cts_b<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><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>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><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>keep<span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</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> 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;XL101112vs789_DESeq2.csv&#x27;</span><span class="hljs-punctuation">)</span><br>rres<br></code></pre></td></tr></table></figure>

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        anchors.removeAll();
        var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
        var res = [];
        for (var item of el) {
          res.push('.markdown-body > ' + item.trim());
        }
        if (CONFIG.anchorjs.placement === 'left') {
          anchors.options.class = 'anchorjs-link-left';
        }
        anchors.add(res.join(', '));
      }
    });
  });
</script>


<script>
  Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
    Fluid.plugins.fancyBox();
  });
</script>


  <script>Fluid.plugins.imageCaption();</script>

  <script  src="/js/local-search.js" ></script>


<!-- 主题的启动项，将它保持在最底部 -->
<!-- the boot of the theme, keep it at the bottom -->
<script  src="/js/boot.js" ></script>


  <noscript>
    <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  </noscript>
<!-- hexo injector body_end start -->
  <script defer src="/theme-inject/timeliness.js"></script>
<!-- hexo injector body_end end --></body>
</html>