COPAR: A ChIP-Seq Optimal Peak Analyzer
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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5357551/ https://www.ncbi.nlm.nih.gov/pubmed/28357402 http://dx.doi.org/10.1155/2017/5346793 |
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author | Tang, Binhua Wang, Xihan Jin, Victor X. |
author_facet | Tang, Binhua Wang, Xihan Jin, Victor X. |
author_sort | Tang, Binhua |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5357551 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Hindawi |
record_format | MEDLINE/PubMed |
spelling | pubmed-53575512017-03-29 COPAR: A ChIP-Seq Optimal Peak Analyzer Tang, Binhua Wang, Xihan Jin, Victor X. Biomed Res Int Research Article 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. Hindawi 2017 2017-03-05 /pmc/articles/PMC5357551/ /pubmed/28357402 http://dx.doi.org/10.1155/2017/5346793 Text en Copyright © 2017 Binhua Tang et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Tang, Binhua Wang, Xihan Jin, Victor X. COPAR: A ChIP-Seq Optimal Peak Analyzer |
title | COPAR: A ChIP-Seq Optimal Peak Analyzer |
title_full | COPAR: A ChIP-Seq Optimal Peak Analyzer |
title_fullStr | COPAR: A ChIP-Seq Optimal Peak Analyzer |
title_full_unstemmed | COPAR: A ChIP-Seq Optimal Peak Analyzer |
title_short | COPAR: A ChIP-Seq Optimal Peak Analyzer |
title_sort | copar: a chip-seq optimal peak analyzer |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5357551/ https://www.ncbi.nlm.nih.gov/pubmed/28357402 http://dx.doi.org/10.1155/2017/5346793 |
work_keys_str_mv | AT tangbinhua coparachipseqoptimalpeakanalyzer AT wangxihan coparachipseqoptimalpeakanalyzer AT jinvictorx coparachipseqoptimalpeakanalyzer |