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…
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技术等。这些技术从不同层次,不同角度,不同维度衡量了非DNA序列对基因转录、表达的调控与影响,使我们进...
~/chipdata$ conda install -y samtools #安装smatools ~/chipdata$ bowtie2-build arabidopsisDNA.fa arabidopsisindex #针对参考基因组建立index文件,并指定前缀名称为arabidopsisindex bowtie2 -p 6 -3 5 --local -x /home/user/chipdata/arabidopsisindex -U chip.fastq | samtools sort -O bam -o /ho...
"ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder." Methods Mol Biol 802: 305-322.Narlikar L, Jothi R (2012) ChIP-Seq data analysis: identification of protein- DNA binding sites with SISSRs peak-finder. Methods Mol Biol 802:305-322....
Computational analysis of ChIP-seq data. Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a new technology to map protein-DNA interactions in a genome. The gen... H Ji - 《Methods in Molecular Biology》
The ChIPettor is designed to stand independently on a 96-deepwell plate while it automatically dispenses, pipettes, and mixes reagents using a pre-programmed ChIP protocol. Validating the ChIPettor In order to control the quality of the ChIPettor system we performed three ChIP-seq experiments on...
scRNA数据分析流程 rna seq数据分析 mRNA-seq数据分析1. 使用fastQC及multiQC对原始测序结果进行质控2. bowtie2去除测序数据中rRNA --约去除0.2%的rRNA数据3. hisat2进行参考基因组比对 --全比对率高于94%证明测序数据质量较好4. samtools转换文件格式5. featureCount对基因表达数据进行定量6. 基因表达数据转化为...
1、根据筛选标准(是否为RNA-seq数据、样本量、样本分类清晰程度、是否有sra原始数据),到GEO数据库中查找数据集。 数据ID:GSE111845 数据来源:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111845 样本介绍:Standard methods were used for RNA-sequencing library construction, EXBead preparation, and...
(ChIP-chip) is increasingly used to map genome-wide-binding sites of transcription factors (TFs), it still remains difficult to generate a quality ChIPx (i.e. ChIP-seq or ChIP-chip) dataset because of the tremendous amount of effort required to develop effective antibodies and efficient ...
RESEARCH ARTICLE Open Access ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis Background: Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or highthroughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such...