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            <h1 id="seo-header">【迁移】从ENI数据库下载fastq文件</h1>
            
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                    Last updated on March 19, 2024 pm
                  
                
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                <h2 id="从-ENI-数据库下载">从 ENI 数据库下载</h2>
<p>进入<a href="https://hexo.limour.top/go/#aHR0cHM6Ly93d3cuZWJpLmFjLnVrL2VuYS9icm93c2VyL3ZpZXcvUFJKTkE1NzM2MDg/c2hvdz1yZWFkcw==" rel="noopener external nofollow noreferrer">ENA Browser</a>，搜索对应的GSE号，进入study项目，选择TSV格式的<strong>Download report</strong>。</p>
<p><img src="https://img.limour.top/2023/09/01/64f1ccc8a3734.webp" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt=""></p>
<p>从TSV表格中提取下载链接，一行一个写入url.txt，前面加上<code>ftp://</code>，接着使用<code>wget -c -i url.txt</code>下载</p>
<p>批量重命名脚本：</p>
<figure class="highlight bash"><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></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-built_in">ls</span> *.fastq.gz | <span class="hljs-built_in">cut</span> -d <span class="hljs-string">&#x27;_&#x27;</span> -f 1 | <span class="hljs-keyword">while</span> <span class="hljs-built_in">read</span> i ;<span class="hljs-keyword">do</span> (<span class="hljs-built_in">echo</span> <span class="hljs-variable">$&#123;i&#125;</span>_1*.gz<span class="hljs-string">&#x27; will be moved to &#x27;</span><span class="hljs-variable">$&#123;i&#125;</span>_S1_L001_R1_001.fastq.gz);<span class="hljs-keyword">done</span><br><span class="hljs-built_in">ls</span> *.fastq.gz | <span class="hljs-built_in">cut</span> -d <span class="hljs-string">&#x27;_&#x27;</span> -f 1 | <span class="hljs-keyword">while</span> <span class="hljs-built_in">read</span> i ;<span class="hljs-keyword">do</span> (<span class="hljs-built_in">echo</span> <span class="hljs-variable">$&#123;i&#125;</span>_2*.gz<span class="hljs-string">&#x27; will be moved to &#x27;</span><span class="hljs-variable">$&#123;i&#125;</span>_S1_L001_R2_001.fastq.gz);<span class="hljs-keyword">done</span><br> <br><span class="hljs-built_in">ls</span> *.fastq.gz | <span class="hljs-built_in">cut</span> -d <span class="hljs-string">&#x27;_&#x27;</span> -f 1 | <span class="hljs-keyword">while</span> <span class="hljs-built_in">read</span> i ;<span class="hljs-keyword">do</span> (<span class="hljs-built_in">mv</span> <span class="hljs-variable">$&#123;i&#125;</span>_1*.gz <span class="hljs-variable">$&#123;i&#125;</span>_S1_L001_R1_001.fastq.gz;<span class="hljs-built_in">mv</span> <span class="hljs-variable">$&#123;i&#125;</span>_2*.gz <span class="hljs-variable">$&#123;i&#125;</span>_S1_L001_R2_001.fastq.gz);<span class="hljs-keyword">done</span><br></code></pre></td></tr></table></figure>
<h2 id="使用-Aspera-下载">使用 Aspera 下载</h2>
<p>Aspera是IBM公司的一款私有专利的高速传输软件，据说能充分利用现有的 WAN 基础设施和通用硬件，传输速度比 FTP 和 HTTP 快达数百倍。</p>
<h3 id="安装aspera">安装aspera</h3>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-comment"># conda create -n linux -c conda-forge tree</span><br>conda activate linux<br>conda install -c hcc aspera-cli -y<br></code></pre></td></tr></table></figure>
<h3 id="获取下载地址">获取下载地址</h3>
<blockquote>
<p>将<code>ftp://ftp.sra.ebi.ac.uk/vol1/</code>之类的地址的前缀<br>
换成<code>era-fasp@fasp.sra.ebi.ac.uk:/vol1/</code></p>
</blockquote>
<h3 id="进行下载">进行下载</h3>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs bash">nano SRR12303173DL.sh &amp;&amp; <span class="hljs-built_in">chmod</span> +x SRR12303173DL.sh<br>./SRR12303173DL.sh<br></code></pre></td></tr></table></figure>
<figure class="highlight bash"><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 bash"><span class="hljs-meta">#!/bin/bash</span><br><span class="hljs-built_in">source</span> activate linux<br>dsa=<span class="hljs-variable">$CONDA_PREFIX</span>/etc/asperaweb_id_dsa.openssh<br>runAscp=<span class="hljs-string">&quot;ascp -qT -l 80m -P 33001 -i <span class="hljs-variable">$dsa</span> era-fasp@fasp.sra.ebi.ac.uk:&quot;</span><br><span class="hljs-comment">#保存路径</span><br>savedir=/home/jovyan/upload/rawData/GSM4685043<br><span class="hljs-built_in">mkdir</span> -p <span class="hljs-variable">$savedir</span><br><span class="hljs-comment">#设置需要下载的文件</span><br><span class="hljs-comment">## SRR12303173</span><br>tempdir=<span class="hljs-variable">$savedir</span><span class="hljs-string">&#x27;/SRR12303173&#x27;</span><br><span class="hljs-built_in">mkdir</span> <span class="hljs-variable">$tempdir</span><br><span class="hljs-variable">$runAscp</span><span class="hljs-string">&#x27;/vol1/fastq/SRR123/073/SRR12303173/SRR12303173_1.fastq.gz&#x27;</span> <span class="hljs-variable">$tempdir</span><span class="hljs-string">&#x27;/dl_1.fastq.gz&#x27;</span><br><span class="hljs-variable">$runAscp</span><span class="hljs-string">&#x27;/vol1/fastq/SRR123/073/SRR12303173/SRR12303173_2.fastq.gz&#x27;</span> <span class="hljs-variable">$tempdir</span><span class="hljs-string">&#x27;/dl_2.fastq.gz&#x27;</span><br></code></pre></td></tr></table></figure>
<ul>
<li>似乎确实挺快的，可以直连，没有不可名状的干扰</li>
</ul>
<h2 id="从-NCBI-数据库下载">从 NCBI 数据库下载</h2>
<h3 id="安装依赖">安装依赖</h3>
<figure class="highlight bash"><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></pre></td><td class="code"><pre><code class="hljs bash">conda create -n sra_tools -c bioconda sra-tools<br>conda activate sra_tools<br>conda install -c conda-forge pigz -y<br>prefetch<br></code></pre></td></tr></table></figure>
<h3 id="批量下载SRA文件">批量下载SRA文件</h3>
<ul>
<li>mkdir upload/zl_liu/sra/GSE172205</li>
<li>cd upload/zl_liu/sra/GSE172205</li>
<li>通过 <a href="https://hexo.limour.top/go/#aHR0cHM6Ly93d3cubmNiaS5ubG0ubmloLmdvdi9nZW8vcXVlcnkvYWNjLmNnaT9hY2M9" rel="noopener external nofollow noreferrer">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=</a>&lt;GSE_ID&gt; 得到 &lt;SRP_ID&gt;</li>
<li>通过 <a href="https://hexo.limour.top/go/#aHR0cHM6Ly93d3cubmNiaS5ubG0ubmloLmdvdi9UcmFjZXMvc3R1ZHkvP2FjYz0=" rel="noopener external nofollow noreferrer">https://www.ncbi.nlm.nih.gov/Traces/study/?acc=</a>&lt;SRP_ID&gt; 搜索 &lt;SRP_ID&gt;</li>
<li>下载 <strong>Total</strong> 的 <strong>Accession List</strong>，上传到 upload/zl_liu/sra/GSE172205 目录下</li>
<li>vdb-config -i 设置http代理，网络好也可以不设置</li>
<li>prefetch --option-file SRR_Acc_List.txt</li>
</ul>
<h3 id="批量转换为FASTQ文件">批量转换为FASTQ文件</h3>
<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>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs bash">nano 11.sh<br><span class="hljs-built_in">chmod</span> +x 11.sh<br>./11.sh<br></code></pre></td></tr></table></figure>
<h2 id="后续分析">后续分析</h2>
<ul>
<li><a href="/STAR--yi-jian-jiao-ben">STAR：一键脚本</a></li>
<li><a href="/shi-yong-GATK-zhao-SNP">使用GATK4.0找SNP</a></li>
<li><a href="/cellranger-ding-liang--One-Library--Multiple-Flowcells">cellranger定量</a></li>
</ul>

                
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