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

BMC Research Notes

Michal Mikula²  Tymon Rubel¹  Krzysztof Goryca²  Krzysztof Chojnowski² 

[1] Warsaw University of Technology, Institute of Radioelectronics, Warsaw 00-665, Poland;Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02-781, Poland

关键词: ChIP-Seq;    Data analysis;    Computational genomics;    Next-generation sequencing;   

Others  :  1127399
DOI  :  10.1186/1756-0500-7-676

 received in 2014-04-15, accepted in 2014-09-23,  发布年份 2014

【 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.

【 授权许可】

   
2014 Chojnowski et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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