Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Bioinformatics. 2014 Nov 15;30(22):3268-9. doi: 10.1093/bioinformatics/btu497. Epub 2014 Jul 30.


Summary: 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.

Availability and implementation: Basic4Cseq is implemented in R and available at A vignette with detailed descriptions of the functions is included in the package.


Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Chromosomes / chemistry
  • High-Throughput Nucleotide Sequencing*
  • Software*