jChIP: A graphical environment for exploratory ChIP-Seq data analysis

被引：2
作者：
Chojnowski K. [1 ]
Goryca K. [1 ]
Rubel T. [2 ]
Mikula M. [1 ]
机构：
[1] Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center, Institute of Oncology, Warsaw
[2] Warsaw University of Technology, Institute of Radioelectronics, Warsaw
来源：
BMC Research Notes | / 7卷 / 1期
关键词：
ChIP-Seq; Computational genomics; Data analysis; Next-generation sequencing;
D O I：
10.1186/1756-0500-7-676
中图分类号：
学科分类号：
摘要：
Background: Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-Seq) provides a powerful tool for discovering protein-DNA interactions. Still, the computational analysis of the great amount of ChIP-Seq data generated, involving mapping of raw data to reference genome, has been a bottle neck for most of researchers in the transcriptional and epigenetic fields. Thus, user-friendly ChIP-Seq processing method sare much needed to enable greater community of computational and bench biologists to exploit the power of ChIP-Seq technology. Findings: jChIP is a graphical tool that was developed to analyze and display ChIP-Seq data. It matches reads to the corresponding loci downloaded from Ensembl Genes or Ensembl Regulation databases. jChIP provides a friendly interface for exploratory analysis of mapped reads as well as peak calling data. The built-in functions for graphical display of reads distribution allows to evaluate the quality and meaning of ChIP-Seq data. Conclusion: jChIP is a user-friendly GUI-based software for the analysis of ChIP-Seq data within context of known genomic features. Further, jChIP provides tools for discovering new and refining known genome-wide protein binding patterns. © 2014 Chojnowski et al.; licensee BioMed Central Ltd.
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