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 loo...

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Detalles Bibliográficos
Autores principales: Li, Guipeng, Chen, Yang, Snyder, Michael P., Zhang, Michael Q.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Methods Online
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224499/
https://www.ncbi.nlm.nih.gov/pubmed/27625391
http://dx.doi.org/10.1093/nar/gkw809
Descripción
Sumario: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.

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