ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis
Copyright policy )ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis
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.
- Stanford University United States
- Harvard University United States
- University of Texas Health Science Center at Dallas United States
- Tsinghua University China (People's Republic of)
- Center for Systems Biology United States
Male, Quality Control, Internet, Base Sequence, Genotype, Genome, Human, Inheritance Patterns, Datasets as Topic, Reproducibility of Results, Sequence Analysis, DNA, Chromatin Assembly and Disassembly, Sensitivity and Specificity, Chromatin, Computer Graphics, Methods Online, Humans, Nucleic Acid Conformation, Female, Alleles, Software
Male, Quality Control, Internet, Base Sequence, Genotype, Genome, Human, Inheritance Patterns, Datasets as Topic, Reproducibility of Results, Sequence Analysis, DNA, Chromatin Assembly and Disassembly, Sensitivity and Specificity, Chromatin, Computer Graphics, Methods Online, Humans, Nucleic Acid Conformation, Female, Alleles, Software
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