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

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NSM-3154-8179.64.pdf (3.78 MB)

Date

2016-09-12

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Oxford University Press

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http://hdl.handle.net/10735.1/6028

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. © The Author(s) 2016.

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Keywords

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

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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].

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

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Zhang, Michael Q.