bwtool: a tool for bigWig files

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.

Fig. 1.

Example of aggregated plots of different histone modification ChIP sequence read-depth signals from MCF7 cells from ENCODE aligned at each of the 20 330 protein-coding gene transcription start sites in GENCODE release v17 (Harrow et al., 2012). See Supplement for instructions on how to reproduce this plot. The raw signals in this example are not normalized, so specific values cannot be compared between signals; however, the morphological differences in averaged profiles are nevertheless useful in characterizing the patterns of each histone mark