bigWig2bedGraph

bigWig2bedGraph converts bigWig files to bedGraph format using standardized genomic windows. Two operation modes are available:

  1. Multiple File Mode: Process batches of files specified in a manifest

  2. Single File Mode: Convert individual bigWig files

Usage:   bigWig2bedGraph [options] ...

Content

Required arguments

-n <windows_name>

Unique identifier for window bins (check available bins with: genomeWindows -l). To create new window bins: 1) bigWig2bedGraph -b <size> -s <species> [...] OR 2) bigWig2bedGraph -b <size> -g <genomesizes> -n <windows_name> [-B <blackList> ...]. [Default: None]

Multiple File Mode

-f <file_list>

Tab-delimited file listing input/output pairs, required for batch mode [Default: None]. Example:

/PATH/TO/H2AFZ_rep1.bw  /PATH/TO/H2AFZ_rep1.bedgraph
/PATH/TO/H2AFZ_rep2.bw  /PATH/TO/H2AFZ_rep2.bedgraph
...

Single File Mode

-i <bigwig>

Input bigWig file, required for single mode. [Default: None]

-o <outfile>

Output bedGraph file, required for single mode. [Default: None]

Optional arguments

-p <nthreads>

Number of parallel processes. [Default: 4]

-z

Output compressed (gzipped) bedGraph files. [Default: false]

-h

Show this help message and exit.

-v

Show program’s version number and exit.

Window Bin Creation

-b <bin_size>

Bin size (in base pairs). [Default: 200]

-s <species>

Supported species: hg38, hg19, or mm10. Selecting this option automatically loads the corresponding genomesizes file and blacklist file. If your species is not listed, manually provide these files via -g <genome_sizes> -n <windows_name> [-B <blackList>]. [Default: None]

-g <genomesizes>

Required if -s is unspecified. Path to a genomesizes file (tab-delimited) listing chromosome lengths [Default: None]. Example:

chr1  249250621
...
-B <blackList>

Path to the blacklist file (tab-delimited). If -s is set to hg38/hg19/mm10, the default blacklist is used [Default: None]. Example:

chr1  200 3000
...