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.
MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing 100084, China.
Guipeng
0000-0002-3244-5499
G
Li
MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing 100084, China.
Yang
Y
Chen
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA mpsnyder@stanford.edu.
Michael P
MP
Snyder
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.|Department of Biological Sciences, Center for Systems Biology, University of Texas, Dallas, 800 West Campbell Road, RL11, Richardson, TX 75080-3021, USA.
Michael Q
MQ
Zhang
D000483:Alleles; D001483:Base Sequence; D002843:Chromatin / Q000737:chemistry* / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D003196:Computer Graphics; D066264:Datasets as Topic; D005260:Female; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D040582:Inheritance Patterns; D020407:Internet; D008297:Male; D009690:Nucleic Acid Conformation; D011786:Quality Control; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D012984:Software
D002843:Chromatin