本实验室可以做的分析：ChIP-seq分析

docs/2024-12/本实验室可以做的分析_ChIP_seq分析.md

@@ -0,0 +1,15 @@
+---
+title: "本实验室可以做的分析：ChIP-seq分析"
+date: 2024-12-15T16:22:49Z
+draft: ["false"]
+tags: [
+  "fetched",
+  "东林的扯淡小屋"
+]
+categories: ["Acdemic"]
+---
+本实验室可以做的分析：ChIP-seq分析 by 东林的扯淡小屋
+------
+<div><section><section><ul><li><li><li><li><li></ul><pre data-lang="bash"><code><span leaf=""><br></span></code><code><span leaf=""><span>ls</span><span> *_R1.fq.gz | </span><span>cut</span><span> -d </span><span>"_"</span><span> -f 1,2 | </span><span>sort</span><span> -u | sed </span><span>'s/_R1.fq.gz//g'</span><span> | </span><span>tr</span><span> </span><span>'\n'</span><span> </span><span>','</span><span> | sed </span><span>'s/,$//'</span></span></code><code><span leaf=""><br></span></code><code><span leaf=""><span>conda activate rnaseq</span></span></code><code><span leaf=""><span>#数据过滤：</span></span></code><code><span leaf=""><span>for i in {};</span></span></code><code><span leaf=""><span>do </span></span></code><code><span leaf=""><span>trim_galore -q 20 --phred33 --stringency 3 --length 20 -e 0.1 --paired ${i}_R1.fq.gz ${i}_R2.fq.gz --gzip -o ./clean -j 50</span></span></code><code><span leaf=""><span>mkdir bowtie2</span></span></code><code><span leaf=""><span>bowtie2 -p 40 -x /data/yudonglin/reference/mouse/mm10/bowtie2/mm10 -1 ./clean/${i}_R1_val_1.fq.gz -2 ./clean/${i}_R2_val_2.fq.gz -S ./bowtie2/${i}_trimmed.sam</span></span></code><code><span leaf=""><span>#sam转换为bam文件</span></span></code><code><span leaf=""><span>grep -v "XS:i:" ./bowtie2/${i}_trimmed.sam |samtools view -bS - &gt;./bowtie2/${i}_trimmed.bam</span></span></code><code><span leaf=""><span>rm ./bowtie2/${i}_trimmed.sam;</span></span></code><code><span leaf=""><span>#bam文件建立索引</span></span></code><code><span leaf=""><span>samtools sort ./bowtie2/${i}_trimmed.bam -o ./bowtie2/${i}_trimmed_sorted.bam</span></span></code><code><span leaf=""><span>samtools index ./bowtie2/${i}_trimmed_sorted.bam</span></span></code><code><span leaf=""><span>#转换为bw文件</span></span></code><code><span leaf=""><span>bamCoverage -b ./bowtie2/${i}_trimmed_sorted.bam -o ./bowtie2/${i}_trimmed_sorted.bam.bw -p 40</span></span></code><code><span leaf=""><span>done</span></span></code><code><span leaf=""><br></span></code><code><span leaf=""><span>#call peak:转录因子</span></span></code><code><span leaf=""><span>macs2 callpeak -t EXPERIMENT_trimmed_sorted.bam -c input_trimmed_sorted.bam -f BAMPE -g mm -n EXPERIMENT -B  -q 0.01</span></span></code><code><span leaf=""><br></span></code><code><span leaf=""><span>#call peak:组蛋白修饰</span></span></code><code><span leaf=""><span>macs2 callpeak -t EXPERIMENT_trimmed_sorted.bam -c NC_trimmed_sorted.bam -f BAMPE -g mm -n EXPERIMENT -B --broad --broad-cutoff 0.1 </span></span></code><code><span leaf=""><br></span></code><code><span leaf=""><span>conda activate homer</span></span></code><code><span leaf=""><span>nohup perl /home/yudonglin/miniconda3/envs/homer/share/homer/bin/findMotifsGenome.pl EXPERIMENT_peaks.broadPeak  mm10 ./EXPERIMENT_motif -S 25 -len 8,10,12,13 -size 400 &amp;</span></span></code><code><span leaf=""><br></span></code><code><span leaf=""><br></span></code></pre></section></section><section nodeleaf=""><img data-ratio="0.1824074074074074" data-s="300,640" data-type="png" data-w="1080" type="block" data-imgfileid="100027915" data-src="https://mmbiz.qpic.cn/mmbiz_png/kZ1wdgAscBr5BkQDPax7Sjjf9ibhhNZlOLrAtjLFv0qFaa7SPuzEgsmQUicLnF5fn8EtIac2FwtibkbNIpAlTpQhw/640?wx_fmt=png&amp;from=appmsg" src="https://mmbiz.qpic.cn/mmbiz_png/kZ1wdgAscBr5BkQDPax7Sjjf9ibhhNZlOLrAtjLFv0qFaa7SPuzEgsmQUicLnF5fn8EtIac2FwtibkbNIpAlTpQhw/640?wx_fmt=png&amp;from=appmsg"></section><section nodeleaf="">可以看转录因子在全基因组范围的结合，也可以看全基因组范围组蛋白修饰的分布，通过实验组和对照组的差异找到可能起到重要调控作用的因子。</section><p><mp-style-type data-value="3"></mp-style-type></p></div>  
+<hr>
+<a href="https://mp.weixin.qq.com/s/VIXSJFWYDryTj0nQ6NT8EA",target="_blank" rel="noopener noreferrer">原文链接</a>