title: jChIP: a graphical environment for exploratory ChIP-Seq data analysis.
abstract: 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 .
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02-781, Poland. krzysiekch@gmail.com.
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Chojnowski
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Goryca
authors.forename: Tymon
authors.initials: T
authors.lastname: Rubel
authors.forename: Michal
authors.initials: M
authors.lastname: Mikula
mesh_terms: D047369:Chromatin Immunoprecipitation; D003196:Computer Graphics; D014584:User-Computer Interface