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

Vida Ravanmehr | Zendy; Minji Kim | Zendy; Zhiying Wang | Zendy; Olgica Milenković | Zendy

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

Author(s) -

Vida Ravanmehr,

Minji Kim,

Zhiying Wang,

Olgica Milenković

Publication year - 2017

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btx685

Subject(s) - lossy compression , lossless compression , computer science , data compression , encode , random access , code (set theory) , algorithm , computer engineering , parallel computing , theoretical computer science , operating system , programming language , chemistry , set (abstract data type) , biochemistry , gene

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.

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