ChIA-PET2

ChIA-PET2 is a comprehensive software pipeline that analyzes various types of ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag Sequencing) data. It streamlines the entire process from raw sequencing reads to the identification of chromatin loops. The pipeline incorporates all the necessary steps, such as linker trimming, read alignment, duplicate removal, peak calling, and chromatin loop calling.

One of the key features of ChIA-PET2 is its versatility and flexibility in handling different ChIA-PET datasets generated from various protocols. It also includes quality control measures at varying stages of the analysis to ensure the reliability of the results.

Moreover, ChIA-PET2 can utilize phased genotype data to identify allele-specific chromatin interactions. The developers have tested ChIA-PET2 on multiple ChIA-PET datasets and demonstrated its improved performance and user-friendly raw data processing.

Topic

Immunoprecipitation experiment;ChIP-seq;DNA packaging;Sequencing;Data quality management

Detail

  • Operation: Peak calling;Nucleic acid sequence analysis

  • Software interface: Command-line user interface

  • Language: R

  • License: GNU General Public License, version 3

  • Cost: Free of charge with restrictions

  • Version name: v0.9.3

  • Credit: The National Basic Research Program of China, National High Technology Research and Development Program of China, National Natural Science Foundation of China, Tsinghua National Laboratory for Information Science and Technology Cross-discipline Foundation, National Institutes of Health.

  • Input: -

  • Output: -

  • Contact: Guipeng Li guipeng.lee@gmail.com

  • Collection: -

  • Maturity: -

Publications

  • ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis.
  • Li G, et al. ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis. ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis. 2017; 45:e4. doi: 10.1093/nar/gkw809
  • https://doi.org/10.1093/NAR/GKW809
  • PMID: 27625391
  • PMC: PMC5224499

Download and documentation

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