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

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dc.contributor.authorLi, G.en_US
dc.contributor.authorChen, Y.en_US
dc.contributor.authorSnyder, M. P.en_US
dc.contributor.authorZhang, Michael Q.en_US
dc.contributor.utdAuthorZhang, Michael Q.en_US
dc.date.accessioned2018-08-24T21:15:15Z
dc.date.available2018-08-24T21:15:15Z
dc.date.created2016-09-12en_US
dc.date.issued2016-09-12en_US
dc.description.abstractChIA-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.en_US
dc.description.departmentSchool of Natural Sciences and Mathematicsen_US
dc.description.sponsorshipNational 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].en_US
dc.identifier.bibliographicCitationLi, 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/gkw809en_US
dc.identifier.issn0305-1048en_US
dc.identifier.issue1en_US
dc.identifier.urihttp://hdl.handle.net/10735.1/6028
dc.identifier.volume45en_US
dc.language.isoenen_US
dc.publisherOxford University Pressen_US
dc.relation.urihttp://dx.doi.org/10.1093/nar/gkw809
dc.rightsCC BY-NC 4.0/ (Attribution-NonCommercial)en_US
dc.rights©2016 The Authorsen_US
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/en_US
dc.sourceNucleic Acids Research
dc.subjectAllelesen_US
dc.subjectBioinformaticsen_US
dc.subjectChromatinen_US
dc.subjectChromosomes--Analysisen_US
dc.subjectQuantitative researchen_US
dc.subjectGenomeen_US
dc.subjectGenotypeen_US
dc.subjectQuality controlen_US
dc.subjectReproducible researchen_US
dc.subjectChemistryen_US
dc.subjectComputer graphicsen_US
dc.subjectConformational analysisen_US
dc.subjectNucleotide sequenceen_US
dc.subjectWomenen_US
dc.subjectHuman beingsen_US
dc.subjectHuman genomeen_US
dc.subjectHeredityen_US
dc.subjectInterneten_US
dc.subjectMenen_US
dc.subjectMetabolismen_US
dc.subjectNucleotide sequenceen_US
dc.titleChIA-PET2: A Versatile and Flexible Pipeline for ChIA-PET Data Analysisen_US
dc.type.genrearticleen_US

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