ChIA-PET2: A Versatile and Flexible Pipeline for ChIA-PET Data Analysis




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Oxford University Press


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 © The Author(s) 2016.



Alleles, Bioinformatics, Chromatin, Chromosomes--Analysis, Quantitative research, Genome, Genotype, Quality control, Reproducible research, Chemistry, Computer graphics, Conformational analysis, Nucleotide sequence, Women, Human beings, Human genome, Heredity, Internet, Men, Metabolism, Nucleotide sequence

National Basic Research Program of China [2012CB316503]; National High Technology Research and Development Program of China [2012AA020401]; National Natural Science Foundation of China [91519326, 31361163004 and 31301044]; National Institutes of Health grants [HG001696, 5U01HG007919-02, 5U54HG00699604 and 5P50HG00773502]. National Basic Research Program of China [2012CB316503].


CC BY-NC 4.0/ (Attribution-NonCommercial), ©2016 The Authors