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  133. <h1 id="seo-header">NCBI-GEO:SRA文件转FASTQ文件</h1>
  134. <div class="markdown-body">
  135. <h2 id="来源"><a href="#来源" class="headerlink" title="来源"></a>来源</h2><p><a target="_blank" rel="noopener" href="https://www.jianshu.com/p/8322e00a9f8a">https://www.jianshu.com/p/8322e00a9f8a</a></p>
  136. <p><a target="_blank" rel="noopener" href="https://zhuanlan.zhihu.com/p/353530857">https://zhuanlan.zhihu.com/p/353530857</a></p>
  137. <p><a target="_blank" rel="noopener" href="https://github.com/rofl0r/proxychains-ng">https://github.com/rofl0r/proxychains-ng</a></p>
  138. <h2 id="通过conda安装纯净环境的sra-tools"><a href="#通过conda安装纯净环境的sra-tools" class="headerlink" title="通过conda安装纯净环境的sra-tools"></a>通过conda安装纯净环境的<strong>sra-tools</strong></h2><ul>
  139. <li><p>conda create -n sra_tools -c bioconda sra-tools</p>
  140. </li>
  141. <li><p>conda activate sra_tools</p>
  142. </li>
  143. <li><p>conda install -c conda-forge pigz -y</p>
  144. </li>
  145. <li><p>prefetch</p>
  146. </li>
  147. <li><p>wget <a target="_blank" rel="noopener" href="https://github.com/rofl0r/proxychains-ng/releases/download/v4.16/proxychains-ng-4.16.tar.xz">https://github.com/rofl0r/proxychains-ng/releases/download/v4.16/proxychains-ng-4.16.tar.xz</a></p>
  148. </li>
  149. <li><p>tar -xvf proxychains-ng-4.16.tar.xz</p>
  150. </li>
  151. <li><p>cd proxychains-ng-4.16</p>
  152. </li>
  153. <li><p>.&#x2F;configure –prefix&#x3D;$HOME&#x2F;dev&#x2F;proxychains4 –sysconfdir&#x3D;$HOME&#x2F;etc</p>
  154. </li>
  155. <li><p>make &amp;&amp; make install</p>
  156. </li>
  157. <li><p>make install-config</p>
  158. </li>
  159. <li><p>添加正确的代理</p>
  160. </li>
  161. <li><p>~&#x2F;dev&#x2F;xray&#x2F;xray -c ~&#x2F;etc&#x2F;xui2.json &amp;</p>
  162. </li>
  163. <li><p>~&#x2F;dev&#x2F;proxychains4&#x2F;bin&#x2F;proxychains4 -f ~&#x2F;etc&#x2F;proxychains.conf curl <a target="_blank" rel="noopener" href="http://www.github.com/">www.github.com</a></p>
  164. </li>
  165. </ul>
  166. <h2 id="批量下载SRA文件"><a href="#批量下载SRA文件" class="headerlink" title="批量下载SRA文件"></a>批量下载SRA文件</h2><ul>
  167. <li>mkdir upload&#x2F;zl_liu&#x2F;sra&#x2F;GSE172205</li>
  168. <li>cd upload&#x2F;zl_liu&#x2F;sra&#x2F;GSE172205</li>
  169. <li>通过 <a target="_blank" rel="noopener" href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=</a>&lt;GSE_ID&gt; 得到 &lt;SRP_ID&gt;</li>
  170. <li>通过 <a target="_blank" rel="noopener" href="https://www.ncbi.nlm.nih.gov/Traces/study/?acc=">https://www.ncbi.nlm.nih.gov/Traces/study/?acc=</a>&lt;SRP_ID&gt; 搜索 &lt;SRP_ID&gt;</li>
  171. <li>下载 <strong>Total</strong> 的 <strong>Accession List</strong>,上传到 upload&#x2F;zl_liu&#x2F;sra&#x2F;GSE172205 目录下</li>
  172. <li> vdb-config -i 设置http代理,网络好也可以不设置</li>
  173. <li>prefetch –option-file SRR_Acc_List.txt</li>
  174. </ul>
  175. <h2 id="批量转换为FASTQ文件"><a href="#批量转换为FASTQ文件" class="headerlink" title="批量转换为FASTQ文件"></a>批量转换为FASTQ文件</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></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=GSE172205<br><span class="hljs-comment">#设置根目录</span><br>ROOTDIR=/home/jovyan/upload/zl_liu/sra/GSE172205<br><span class="hljs-comment">#设置CleanData存放目录</span><br>CLEAN=<span class="hljs-variable">$ROOTDIR</span>/<span class="hljs-variable">$TASKN</span><br> <br><span class="hljs-built_in">mkdir</span> <span class="hljs-variable">$CLEAN</span><br><span class="hljs-keyword">for</span> file <span class="hljs-keyword">in</span> `<span class="hljs-built_in">cat</span> SRR_Acc_List.txt`<br><span class="hljs-keyword">do</span><br><span class="hljs-built_in">echo</span> <span class="hljs-variable">$file</span><br><span class="hljs-built_in">mkdir</span> <span class="hljs-variable">$CLEAN</span>/<span class="hljs-variable">$file</span><br><span class="hljs-built_in">cd</span> <span class="hljs-variable">$CLEAN</span>/<span class="hljs-variable">$file</span><br>fasterq-dump --split-3 <span class="hljs-variable">$ROOTDIR</span>/<span class="hljs-variable">$file</span> -e 16<br>pigz -p 16 *<br><span class="hljs-keyword">done</span><br></code></pre></td></tr></table></figure>
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