本实验室可以做的分析：AmpliconArchitect鉴定WGS数据的eccDNA

docs/2024-12/本实验室可以做的分析_AmpliconArchitect鉴定WGS数据的eccDNA.md

@@ -0,0 +1,15 @@
+---
+title: "本实验室可以做的分析：AmpliconArchitect鉴定WGS数据的eccDNA"
+date: 2024-12-14T00:30:54Z
+draft: ["false"]
+tags: [
+  "fetched",
+  "东林的扯淡小屋"
+]
+categories: ["Acdemic"]
+---
+本实验室可以做的分析：AmpliconArchitect鉴定WGS数据的eccDNA by 东林的扯淡小屋
+------
+<div><section><section><ul><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li><li></ul><pre data-lang="swift"><code><span leaf=""><span>#构建虚拟环境并进行</span></span></code><code><span leaf=""><span>conda create </span><span>--</span><span>name </span><span>WGS</span><span> python</span><span>==</span><span>3.10</span><span>.</span><span>6</span></span></code><code><span leaf=""><span>#source activate </span><span>WGS</span></span></code><code><span leaf=""><span>conda activate </span><span>WGS</span></span></code><code><span leaf=""><span>#</span><span>Installation</span><span> using conda:</span></span></code><code><span leaf=""><span>conda install cnvkit</span><span>==</span><span>0.9</span><span>.</span><span>10</span></span></code><code><span leaf=""><span>conda install bowtie2 </span><span>-</span><span>y</span></span></code><code><span leaf=""><span>conda install bedtools </span><span>-</span><span>y</span></span></code><code><span leaf=""><span>conda install samtools </span><span>-</span><span>y</span></span></code><code><span leaf=""><span>conda install parallel </span><span>-</span><span>y</span></span></code><code><span leaf=""><span>conda install bwa </span><span>-</span><span>y</span></span></code><code><span leaf=""><span>conda install samblaster </span><span>-</span><span>y</span></span></code><code><span leaf=""><span>conda install gatk</span></span></code><code><span leaf=""><span>pip install intervaltree</span></span></code><code><span leaf=""><span>pip install scipy</span></span></code><code><span leaf=""><span>pip install matplotlib</span></span></code><code><span leaf=""><span>cd </span><span>/data/</span><span>yudonglin</span><span>/data/</span><span>WGS</span><span>/mao</span></span></code><code><span leaf=""><span>cd /data</span><span>/yudonglin/</span><span>software</span><span>/AmpliconArchitect/</span></span></code><code><span leaf=""><span>conda activate </span><span>WGS</span></span></code><code><span leaf=""><span>cd </span><span>AmpliconClassifier</span></span></code><code><span leaf=""><span>echo export </span><span>AC_SRC</span><span>=</span><span>$PWD</span><span> </span><span>&gt;&gt;</span><span> </span><span>~/</span><span>.bashrc</span></span></code><code><span leaf=""><span>source </span><span>~/</span><span>.bashrc</span></span></code><code><span leaf=""><span>export </span><span>MOSEKLM_LICENSE_FILE</span><span>=/</span><span>data</span><span>/yudonglin/</span><span>software</span><span>/AmpliconArchitect/</span><span> </span><span>&gt;&gt;</span><span> </span><span>~/</span><span>.bashrc </span><span>&amp;&amp;</span><span> source </span><span>~/</span><span>.bashrc</span></span></code><code><span leaf=""><span>cd </span><span>/data/</span><span>yudonglin</span><span>/software/</span><span>AmpliconArchitect</span><span>/</span></span></code><code><span leaf=""><span>echo export AA_SRC=$PWD/src </span><span>&gt;&gt;</span><span> </span><span>~/</span><span>.bashrc</span></span></code><code><span leaf=""><span>cd </span><span>/data/</span><span>yudonglin</span><span>/software/</span><span>AmpliconArchitect</span><span>/data_repo</span></span></code><code><span leaf=""><span>echo export AA_DATA_REPO=$PWD &gt;&gt; ~/.bashrc</span></span></code><code><span leaf=""><span>cd </span><span>$AA_DATA_REPO</span><span> </span><span>&amp;&amp;</span><span> touch coverage.stats </span><span>&amp;&amp;</span><span> chmod a</span><span>+</span><span>r coverage.stats</span></span></code><code><span leaf=""><span>source </span><span>~/</span><span>.bashrc</span></span></code><code><span leaf=""><span>cd </span><span>/data/</span><span>yudonglin</span><span>/software/</span><span>AmpliconArchitect</span></span></code><code><span leaf=""><span>AA</span><span>=/</span><span>data</span><span>/yudonglin/</span><span>software</span><span>/AmpliconArchitect/</span><span>docker</span><span>/run_aa_docker.sh</span></span></code><code><span leaf=""><span>export LD_LIBRARY_PATH=/data</span><span>/yudonglin/</span><span>software</span><span>/mosek/</span><span>8</span><span>/tools/</span><span>platform</span><span>/linux64x86/</span><span>bin:</span><span>$LD_LIBRARY_PATH</span><span>&gt;&gt;</span><span> </span><span>~/</span><span>.bashrc </span><span>&amp;&amp;</span><span> source </span><span>~/</span><span>.bashrc </span></span></code><code><span leaf=""><span>#</span><span>./</span><span>software</span><span>/mosek/</span><span>8</span><span>/tools/</span><span>platform</span><span>/linux64x86/</span><span>bin</span><span>/libmosekxx8_0.so</span></span></code><code><span leaf=""><span>env |grep DATA</span></span></code><code><span leaf=""><span>env |grep MOSEK</span></span></code><code><span leaf=""><span>echo $AA</span></span></code><code><span leaf=""><span>#直接下载数据</span></span></code><code><span leaf=""><span>fastq-dump -I --split-3 --gzip SRR8670694 </span></span></code><code><span leaf=""><span>trim_galore -q 25 --phred33 --length 36 --paired  -j 30 SRR8670694_1.fastq.gz SRR8670694_2.fastq.gz  -o ./clean</span></span></code><code><span leaf=""><span>#成功运行：</span></span></code><code><span leaf=""><span>cd </span><span>/data/</span><span>yudonglin</span><span>/data/</span><span>WGS</span><span>/mao/</span><span>clean</span></span></code><code><span leaf=""><span>conda activate </span><span>WGS</span></span></code><code><span leaf=""><span>python </span><span>/data/</span><span>yudonglin</span><span>/software/</span><span>AmpliconArchitect</span><span>/AmpliconSuite-pipeline/</span><span>PrepareAA</span><span>.py </span><span>-</span><span>s </span><span>SRR8670768_sample</span><span>  </span><span>-</span><span>t </span><span>60</span><span> </span><span>--</span><span>cnvkit_dir </span><span>/home/</span><span>yudonglin</span><span>/miniconda3/</span><span>envs</span><span>/WGS/</span><span>bin</span><span>/</span><span>cnvkit.py </span><span>--</span><span>fastqs </span><span>SRR8670768_1_val_1</span><span>.fq.gz </span><span>SRR8670768_2_val_2</span><span>.fq.gz </span><span>--</span><span>ref hg38 </span><span>--</span><span>run_AA</span></span></code><code><span leaf=""><br></span></code></pre></section></section><section nodeleaf=""><img data-imgfileid="100027829" data-ratio="0.5935185185185186" data-s="300,640" data-src="https://mmbiz.qpic.cn/mmbiz_png/kZ1wdgAscBricicFNLOEKibZHMftxcVVu2JxyBT3acWNZr3jxHXViavJQOLAX2BVibOYDeAPhiceaXaHpThibPlnnnHTA/640?wx_fmt=png&amp;from=appmsg" data-type="png" data-w="1080" type="block" src="https://mmbiz.qpic.cn/mmbiz_png/kZ1wdgAscBricicFNLOEKibZHMftxcVVu2JxyBT3acWNZr3jxHXViavJQOLAX2BVibOYDeAPhiceaXaHpThibPlnnnHTA/640?wx_fmt=png&amp;from=appmsg"></section><section nodeleaf=""><img data-src="https://mmbiz.qpic.cn/mmbiz_png/kZ1wdgAscBqTRWBb24ibv0mwUyII7cAuNaEibWucny7PLWG0iaIbFqKtg8o8nM2rIodFLn5XrwGZoYrAkvh838msw/640?wx_fmt=png&amp;from=appmsg" data-ratio="0.41574074074074074" data-s="300,640" data-type="png" data-w="1080" type="block" data-imgfileid="100027895" src="https://mmbiz.qpic.cn/mmbiz_png/kZ1wdgAscBqTRWBb24ibv0mwUyII7cAuNaEibWucny7PLWG0iaIbFqKtg8o8nM2rIodFLn5XrwGZoYrAkvh838msw/640?wx_fmt=png&amp;from=appmsg"></section><section nodeleaf=""><img data-src="https://mmbiz.qpic.cn/mmbiz_png/kZ1wdgAscBpWjxwnR6d7E1MranaeicibMQPQZUbSS8CVyiaQjrekyZt5WlJ4WFrU0B15ick8PRCZPZ1vFEHI5orVpg/640?wx_fmt=png&amp;from=appmsg" data-ratio="0.2064814814814815" data-s="300,640" data-type="png" data-w="1080" type="block" data-imgfileid="100027902" src="https://mmbiz.qpic.cn/mmbiz_png/kZ1wdgAscBpWjxwnR6d7E1MranaeicibMQPQZUbSS8CVyiaQjrekyZt5WlJ4WFrU0B15ick8PRCZPZ1vFEHI5orVpg/640?wx_fmt=png&amp;from=appmsg"></section><section><span leaf="">所以我们可以通过鉴定任意WGS的数据，鉴定其中是否具有eccDNA了！可能在肿瘤的发生发展乃至于转移过程中发生重要的作用。接下来我只需要做好数据收集工作就行了。</span></section><p><mp-style-type data-value="3"></mp-style-type></p></div>  
+<hr>
+<a href="https://mp.weixin.qq.com/s/ZwTpcgE8CWHAsjGBA_M0ig",target="_blank" rel="noopener noreferrer">原文链接</a>