ChIP-Seq data analysis is often a cumbersome process, requiring tedious project setup and time-consuming, complicated data manipulation.Lasergene Genomicsmakes it quick and easy to set up your ChIP-Seq analysis project, by offering an easy-to-use wizard that guides you through project setup in m...
1 ChIP-Seq技术 1.1 概念 1.2 ChIP-seq技术原理 2 ChIP-Seq数据分析 2.1 数据下载 2.2 质量控制(data_assess) 2.3 比对到参考基因组(mapping_analysis) 2.4 搜峰(Peak_calling) MACS2 2.4.1 MAC
DATA_SRA_DIR="data_sra" DATA_FASTQ_DIR="data_fastq" # 创建输出目录 mkdir -p ${DATA_FASTQ_DIR} cd $DATA_SRA_DIR # 读取down_load.list文件,并下载每个SRA文件 while IFS= read -r sra_id do # 使用prefetch下载SRA文件到指定目录 prefetch $sra_id # 使用fasterq-dump转换SRA文件为fastq.gz格式...
ChIP-Seq Data AnalysisAnalyzer, Illumina Genome
1,Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data 文章从数据质控,比对,peak calling,peak注释,motif分析都给出了注意点,值得一读 论文从数据的质控到最后的peak注释都给了很多说明。 2,硕士论文 基于ChIP-seq全基因组识别毛竹笋尖与鞭笋尖组蛋白修饰位点 ...
这篇2011年的文章对ChIP-Seq的分析流程进行比较详细的讲解,个人读完后对ChIP数据质量控制和可信度提高上有了更多的认识,但之后的call-peak和peak注释作者主要是介绍一款名为CisGenome的软件计算原理和优点,然而…
install bwa-y #安装bwa~/src$ conda install fastqc trimmomatic #安装fastqc和trimmomatic包~$ cd chipdata~/chipdata$ fastqc*.fastq #对获得的fastq原始数据进行qc并输出报告Startedanalysis of chip.fastqApprox5%completeforchip.fastqApprox10%completeforchip.fastqApprox15%completeforchip.fastqApprox20%complete...
cd/data/gy/project/epi/clean #改成自己的 analysis_dir=/data/gy/project/epi bin_trim_galore="trim_galore"ls../raw/*gz | while read fq1; do nohup $bin_trim_galore -q 25 --phred33 --length 25 -e 0.1 --stringency 4 -o $analysis_dir/clean $fq1 & ...
虽然ChIPseeker是我写给自己做ChIPseq注释的,但Ming Tang (https://github.com/crazyhottommy/ChIP-seq-analysis)用它去做DNA breakdown注释,当然像lincRNA注释也是有人做并且完全是支持的。有一些我以前从没在文档里提到的东西,也应该会在这个系列里写出来。
Data analysisSequencingWorkflowThe development of novel high-throughput sequencing methods for ChIP (chromatin immunoprecipitation) has provided a very powerful tool to study gene regulation in multiple conditions at unprecedented resolution and scale. Proactive quality-control and appropriate data analysis ...