copar: a chip-seq optimal peak analyzer
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2017
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Abstract
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.
| Reference Key |
tang2017biomedcopar:
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|---|---|
| Authors | ;Binhua Tang;Xihan Wang;Victor X. Jin |
| Journal | spectrochimica acta - part a: molecular and biomolecular spectroscopy |
| Year | 2017 |
| DOI |
10.1155/2017/5346793
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