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Bioinformatics. 2014 Jun 1;30(11):1618-9. doi: 10.1093/bioinformatics/btu056. Epub 2014 Jan 30.

bwtool: a tool for bigWig files.

Author information

1
Department of Gene Regulation, Stem Cells, and Cancer, Centre for Genomic Regulation (CRG) and Department of Experimental and Health Sciences (CEXS), Universitat Pompeu Fabra, 08003 Barcelona, SpainDepartment of Gene Regulation, Stem Cells, and Cancer, Centre for Genomic Regulation (CRG) and Department of Experimental and Health Sciences (CEXS), Universitat Pompeu Fabra, 08003 Barcelona, Spain.

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.

AVAILABILITY AND IMPLEMENTATION:

The C source code is freely available under the GNU public license v3 at http://cromatina.crg.eu/bwtool.

PMID:
24489365
PMCID:
PMC4029031
DOI:
10.1093/bioinformatics/btu056
[Indexed for MEDLINE]
Free PMC Article

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