title: Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data.
abstract: CONCLUSIONS
  Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. The package processes aligned 4C-seq raw data stored in binary alignment/map (BAM) format and maps the short reads to a corresponding virtual fragment library. Functions are included to create virtual fragment libraries providing chromosome position and further information on 4C-seq fragments (length and uniqueness of the fragment ends, and blindness of a fragment) for any BSGenome package. An optional filter is included for BAM files to remove invalid 4C-seq reads, and further filter functions are offered for 4C-seq fragments. Additionally, basic quality controls based on the read distribution are included. Fragment data in the vicinity of the experiment's viewpoint are visualized as coverage plot based on a running median approach and a multi-scale contact profile. Wig files or csv files of the fragment data can be exported for further analyses and visualizations of interactions with other programs.
  
  
  METHODS
  Basic4Cseq is implemented in R and available at http://www.bioconductor.org/. A vignette with detailed descriptions of the functions is included in the package.
  
  
  BACKGROUND
  Carolin.Walter@uni-muenster.de
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Institute of Medical Informatics, University of Münster, 48149 Münster, Germany, and Institute of Molecular Tumorbiology, University of Münster, 48149 Münster, Germany.
authors: Carolin
authors: C
authors: Walter
authors: Institute of Medical Informatics, University of Münster, 48149 Münster, Germany, and Institute of Molecular Tumorbiology, University of Münster, 48149 Münster, Germany.
authors: Daniel
authors: D
authors: Schuetzmann
authors: Institute of Medical Informatics, University of Münster, 48149 Münster, Germany, and Institute of Molecular Tumorbiology, University of Münster, 48149 Münster, Germany.
authors: Frank
authors: F
authors: Rosenbauer
authors: Institute of Medical Informatics, University of Münster, 48149 Münster, Germany, and Institute of Molecular Tumorbiology, University of Münster, 48149 Münster, Germany.
authors: Martin
authors: M
authors: Dugas
mesh_terms: D002875:Chromosomes / Q000737:chemistry; D059014:High-Throughput Nucleotide Sequencing; D012984:Software