bwtool: a tool for bigWig files

Pohl, Andy, 1979-; Beato, Miguel

doi:http://dx.doi.org/10.1093/bioinformatics/btu056

bwtool: a tool for bigWig files

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Citation

Pohl A, Beato M. bwtool: a tool for bigWig files. Bioinformatics. 2014; 30(11):1618-9. DOI: 10.1093/bioinformatics/btu056

Abstract

BigWig files are a compressed, indexed, binary format for genome-wide signal data for calculations (e.g. GC percent) or experiments (e.g. ChIP-seq/RNA-seq read depth). bwtool is a tool designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions. Additionally, the tool enables the conversion of the positions of signal data from one genome assembly to another, also known as 'lifting'. We believe bwtool can be useful for the analyst frequently working with bigWig data, which is becoming a standard format to represent functional signals along genomes. The article includes supplementary examples of running the software.