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

• Published in: Bioinformatics (Oxford, England) England), 2014-11, Vol.30 (22), p.3268-3269
• Main Authors: Walter, Carolin, Schuetzmann, Daniel, Rosenbauer, Frank, Dugas, Martin
• Format: Article
• Language: English
• Subjects: Chromosomes - chemistry; High-Throughput Nucleotide Sequencing; Software
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btu497

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. 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. [e-mail] Supplementary data are available at Bioinformatics online.