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

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

Author information

1
MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing 100084, China.
2
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA mpsnyder@stanford.edu.
3
MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing 100084, China michael.zhang@utdallas.edu.
4
Department of Biological Sciences, Center for Systems Biology, University of Texas, Dallas, 800 West Campbell Road, RL11, Richardson, TX 75080-3021, USA.

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.

PMID:
27625391
PMCID:
PMC5224499
DOI:
10.1093/nar/gkw809
[Indexed for MEDLINE]
Free PMC Article

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