HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data

管道(软件) 计算机科学 工作流程 注释 DNA微阵列 生物导体 计算生物学 炸薯条 数据挖掘 软件 染色质免疫沉淀 基因组浏览器 基因组学 数据库 生物 基因组 遗传学 人工智能 基因 程序设计语言 电信 基因表达 发起人
作者
Huihuang Yan,Jared M. Evans,Mike Kalmbach,Raymond M. Moore,Sumit Middha,Stanislav Luban,Liguo Wang,Aditya Bhagwate,Ying Li,Zhifu Sun,Xianfeng Chen,Jean‐Pierre Kocher
出处
期刊:BMC Bioinformatics [BioMed Central]
卷期号:15 (1) 被引量:57
标识
DOI:10.1186/1471-2105-15-280
摘要

Chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (ChIP-Seq) has been widely used to identify genomic loci of transcription factor (TF) binding and histone modifications. ChIP-Seq data analysis involves multiple steps from read mapping and peak calling to data integration and interpretation. It remains challenging and time-consuming to process large amounts of ChIP-Seq data derived from different antibodies or experimental designs using the same approach. To address this challenge, there is a need for a comprehensive analysis pipeline with flexible settings to accelerate the utilization of this powerful technology in epigenetics research.We have developed a highly integrative pipeline, termed HiChIP for systematic analysis of ChIP-Seq data. HiChIP incorporates several open source software packages selected based on internal assessments and published comparisons. It also includes a set of tools developed in-house. This workflow enables the analysis of both paired-end and single-end ChIP-Seq reads, with or without replicates for the characterization and annotation of both punctate and diffuse binding sites. The main functionality of HiChIP includes: (a) read quality checking; (b) read mapping and filtering; (c) peak calling and peak consistency analysis; and (d) result visualization. In addition, this pipeline contains modules for generating binding profiles over selected genomic features, de novo motif finding from transcription factor (TF) binding sites and functional annotation of peak associated genes.HiChIP is a comprehensive analysis pipeline that can be configured to analyze ChIP-Seq data derived from varying antibodies and experiment designs. Using public ChIP-Seq data we demonstrate that HiChIP is a fast and reliable pipeline for processing large amounts of ChIP-Seq data.
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