ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis

Nucleic Acids Res. 2017 Jan 9;45(1):e4. doi: 10.1093/nar/gkw809. Epub 2016 Sep 12.

Abstract

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, read alignment, duplicate removal, peak calling and chromatin loop calling. It supports different kinds of ChIA-PET data generated from different ChIA-PET protocols and also provides quality controls for different steps of ChIA-PET analysis. In addition, ChIA-PET2 can use phased genotype data to call allele-specific chromatin interactions. We applied ChIA-PET2 to different ChIA-PET datasets, demonstrating its significantly improved performance as well as its ability to easily process ChIA-PET raw data. ChIA-PET2 is available at https://github.com/GuipengLi/ChIA-PET2.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles*
  • Base Sequence
  • Chromatin / chemistry*
  • Chromatin / metabolism
  • Chromatin Assembly and Disassembly*
  • Computer Graphics
  • Datasets as Topic
  • Female
  • Genome, Human
  • Genotype
  • Humans
  • Inheritance Patterns*
  • Internet
  • Male
  • Nucleic Acid Conformation
  • Quality Control
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Sequence Analysis, DNA
  • Software*

Substances

  • Chromatin