Introduction

Sequencing data quality and peak alignment efficiency of ChIP-sequencing profiles are directly related to the reliability and reproducibility of NGS experiments. Till now, there is no tool specifically designed for optimal peak alignment estimation and quality-related genomic feature extraction for ChIP-sequencing profiles. We developed open-sourced COPAR, a user-friendly package, to statistically investigate, quantify, and visualize the optimal peak alignment and inherent genomic features using ChIP-seq data from NGS experiments. It provides a versatile perspective for biologists to perform quality-check for high-throughput experiments and optimize their experiment design. The package COPAR can process mapped ChIP-seq read file in BED format and output statistically sound results for multiple high-throughput experiments. Together with three public ChIP-seq data sets verified with the developed package, we have deposited COPAR on GitHub under a GNU GPL license.

Publications

  1. COPAR: A ChIP-Seq Optimal Peak Analyzer.
    Cite this
    Tang B, Wang X, Jin VX, 2017-01-01 - BioMed research international

Credits

  1. Binhua Tang
    Developer

    Epigenetics & Function Group, School of Internet of Things, China

  2. Xihan Wang
    Developer

    Epigenetics & Function Group, School of Internet of Things, China

  3. Victor X Jin
    Investigator

    Department of Molecular Medicine & Biostatistics, University of Texas Health Science Center, United States of America

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Summary
AccessionBT002144
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByVictor X Jin