ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data.

ABSTRACT: Motivation:Chromatin immunoprecipitation sequencing (ChIP-seq) experiments are inexpensive and time-efficient, and result in massive datasets that introduce significant storage and maintenance challenges. To address the resulting Big Data problems, we propose a lossless and lossy compression framework specifically designed for ChIP-seq Wig data, termed ChIPWig. ChIPWig enables random access, summary statistics lookups and it is based on the asymptotic theory of optimal point density design for nonuniform quantizers. Results:We tested the ChIPWig compressor on 10 ChIP-seq datasets generated by the ENCODE consortium. On average, 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 r

SUBMITTER: Ravanmehr V 

PROVIDER: S-EPMC5860022 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature