1 测序数据分析流程 原始数据FastQ文件1.数据预处理 数据文件FastQ文件2.序列比对 mappingfile3.数据分析 初步结果4.GOanalysis 进一步的结果 ChIP-SeqRNA-SeqChIA-PET。。。2 基因转录调控 •基因转录中，有很多因子参与调控 –基因启动子–近程调控元件–远程调控元件 3 基因转录调控 •基因转录中，有很多因子...
ChIA-PET2 is a versatile and flexible pipeline for analyzing different types of ChIA-PET data from raw sequencing reads to chromatin loops. ChIA-PET2 integrates all steps required for ChIA-PET data analysis, including linker trimming, re... G Li,Y Chen,MP Snyder,... - 《Nucleic Acids Res...
Advances in computational ChIA-PET data analysis. Quantitative Biology 4(217) (2016).Li G, Chen Y, Snyder MP, Zhang MQ. ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis. Nucleic Acids Res. 2017;45:e4.Li, G., Chen, Y., Snyder, M. P. & Zhang, M. Q. ...
ChIA-PET2 is a versatile and flexible pipeline for analysing different variants of ChIA-PET data from raw sequencing reads to chromatin loops.ChIA-PET2 was named not only because it is a tool for ChIA-PET data analysis, but also because it supports at least 2 different ChIA-PET protocols ...
Interpretation of ChIA-PET data requires a robust analytic pipeline. Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, visualization, and analysis. ChIA-PIPE performs linker filtering, read mapping, peak calling, and loop calling and automate...
1. Will the server roles be split up and allow for assigning different machines to those various roles (e.g., master server, proxy server, world server, database server)? 2. Will dynamic load balancing and fault tolerance still be implemented? That was a conversation on these forums a lon...
Before executing theChIAMM, you need to analyze the raw ChIA-PET data using ChIA-PET Tool V3 without any FDR cutoff value. From the ChIA-PET Tool output files, the file out.cluster.withpvalue.txt will be used for downstream analysis in ChIAMM. Specifically, the first 11 columns in the...
A computational method for accurately predicting ChIA-PET interactions from Hi-C and ChIP-seq data is needed that can save the efforts of performing wet-lab experiments. Here we present DeepChIA-PET, a supervised deep learning approach that can accurately predict ChIA...
A typical read spread function estimated from RNA PolII ChIA-PET data.Christopher ReederMichael ClosserHuay Mei PohKuljeet SandhuHynek WichterleDavid Gifford
CYTOBAND_DATA ChIA-PET_Tool_V3/chromInfo/hg19_cytoBandIdeo.txt --SPECIES 1 --INPUT_ANCHOR_FILE Anchor.bed --output Output_GM12878 --prefix GM12878_MCF7 java -jar ChIA-PET.jar --mode 1 --fastq1 MCF7_1.fastq --fastq2 MCF7_2.fastq --linker ChIA-PET_Tool_V3/linker/linker_long.txt...