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...
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...
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
应用第二代测序技术,科学家们针对不同层次的转录调控阶段开发了等一系列测序技术进行研究,硕果累累。比如,针对DNA结合蛋白在全基因组结合位点分布的探索,开发了ChIP-seq技术;针对染色质开放程度的衡量,开发了DNase-seq,ATAC-seq技术;针对基因组甲基化水平的探索,开发了BS-seq;针对三维层次的调控研究,开发了Hi-C技术...
DiffBind Differential binding analysis of ChIP-Seq peak data:ChIP-seq数据峰值diffbind结合差异分析 热度: Peak identification for ChIP-seq data with no controls 热度: 染色质免疫共沉淀-测序(ChIP-Seq)技术及数据分析方法介绍 Introduction of ChIP-Seq Technology and Data Analysis ...
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 $fq1 & ...
1,Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data 文章从数据质控,比对,peak calling,peak注释,motif分析都给出了注意点,值得一读 论文从数据的质控到最后的peak注释都给了很多说明。 2,硕士论文 基于ChIP-seq全基因组识别毛竹笋尖与鞭笋尖组蛋白修饰位点 ...
install bwa-y #安装bwa~/src$ 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...
ChIP-Seq Data AnalysisAnalyzer, Illumina Genome
Large-scale quality analysis of published ChIPseq data. Marinov GK, Kundaje A, Park PJ, Wold BJ. G3 (Bethesda). 2014 Feb 19;4(2) ChIPseq 中人工制品重复的高估。 Systematic evaluation of factors influencing ChIPseq fidelity.Nat Methods. Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery...