w4CSeq

w4CSeq is a software and web application designed to analyze 4C-seq data. It enables researchers to identify genome-wide partners interacting with a specific locus through a statistical approach. The user-friendly interface allows users to upload raw 4C sequencing data (FASTQ files) and receive results, including a list of candidate interacting sites/regions, visualizations of genome-wide distribution of interacting regions, and analysis of enrichment of features such as TSSs, TTSs, CpG sites, and DNA replication timing.

Topic

DNA structural variation;Sequencing

Detail

  • Operation: Sequence analysis

  • Software interface: Command-line user interface;Web user interface

  • Language: R;Javascript;Perl

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: -

  • Credit: National Institutes of Health (NIH).

  • Input: -

  • Output: .bed, .bam, .pdf, .png

  • Contact: Mingyang Cai caimingyang08nju@gmail.com, Kai Wang kaichop@gmail.com

  • Collection: -

  • Maturity: -

Publications

  • w4CSeq: software and web application to analyze 4C-seq data.
  • Cai M, et al. w4CSeq: software and web application to analyze 4C-seq data. w4CSeq: software and web application to analyze 4C-seq data. 2016; 32:3333-3335. doi: 10.1093/bioinformatics/btw408
  • https://doi.org/10.1093/bioinformatics/btw408
  • PMID: 27378289
  • PMC: PMC5079477

Download and documentation

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