ChIPWig

'ChIPWig' is a software tool designed for compressing and storing ChIP-seq Wig data. It is based on the asymptotic theory of optimal point density design and enables random access and summary statistics lookups. Testing on 10 ChIP-seq datasets generated by the ENCODE consortium, lossless ChIPWig reduced the file sizes to merely 6% of the original, and offered 6-fold compression rate improvement compared to bigWig. The lossy feature further reduced file sizes 2-fold compared to the lossless mode, with little or no effects on peak calling and motif discovery using specialized NarrowPeaks methods.

Topic

ChIP-seq;Data governance;Laboratory information management

Detail

  • Operation: Formatting

  • Software interface: Library

  • Language: C++

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: The National Institutes of Health (NIH) Big Data to Knowledge Targeted Software Development program, the National Science Foundation (NSF) Emerging Frontiers for Science of Information Center, NSF Graduate Research Fellowship Program.

  • Input: -

  • Output: -

  • Contact: milenkov@illinois.edu

  • Collection: -

  • Maturity: -

Publications

  • ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data.
  • Ravanmehr V, et al. ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data. ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data. 2018; 34:911-919. doi: 10.1093/bioinformatics/btx685
  • https://doi.org/10.1093/bioinformatics/btx685
  • PMID: 29087447
  • PMC: PMC5860022

Download and documentation

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