Mango: a bias-correcting ChIA-PET analysis pipeline | Zendy

Douglas H. Phanstiel | Zendy; Alan P. Boyle | Zendy; Nastaran Heidari | Zendy; M Snyder | Zendy

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Mango: a bias-correcting ChIA-PET analysis pipeline

Author(s) -

Douglas H. Phanstiel,

Alan P. Boyle,

Nastaran Heidari,

M Snyder

Publication year - 2015

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btv336

Subject(s) - ctcf , pipeline (software) , computer science , software , r package , genome , computational biology , data mining , biology , genetics , gene , gene expression , computational science , enhancer , programming language

Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established method for detecting genome-wide looping interactions at high resolution. Current ChIA-PET analysis software packages either fail to correct for non-specific interactions due to genomic proximity or only address a fraction of the steps required for data processing. We present Mango, a complete ChIA-PET data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic proximity.

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