Li, G.Chen, Y.Snyder, M. P.Zhang, Michael Q.2018-08-242018-08-242016-09-122016-09-120305-1048http://hdl.handle.net/10735.1/6028ChIA-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.enCC BY-NC 4.0/ (Attribution-NonCommercial)©2016 The Authorshttp://creativecommons.org/licenses/by-nc/4.0/AllelesBioinformaticsChromatinChromosomes--AnalysisQuantitative researchGenomeGenotypeQuality controlReproducible researchChemistryComputer graphicsConformational analysisNucleotide sequenceWomenHuman beingsHuman genomeHeredityInternetMenMetabolismNucleotide sequencearticleLi, G., Y. Chen, M. P. Snyder, and M. Q. Zhang. 2017. "ChIA-PET2: A versatile and flexible pipeline for ChIA-PET data analysis; 27625391." Nucleic Acids Research 45(1), doi:10.1093/nar/gkw809451