bedGraph2bigWig

bedGraph2bigWig is a tool to convert bedgraph file format to bigwig file format. Two operation modes are available:

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

  2. Single File Mode: Convert individual bedgraph files

Usage: bedGraph2bigWig [options] ...

Content

Required arguments

-s <species>

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

-g <genomesizes>

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

chr1  249250621
...

Multiple File Mode

-f <file_list>

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

/PATH/TO/example1.bedgraph       /PATH/TO/example1.bw
/PATH/TO/example2.bedgraph       /PATH/TO/example2.bw
...

Single File Mode

-i <bedgraph>

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

-o <outfile>

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

Optional arguments

-p <nthreads>

Number of parallel processes. [Default: 4]

-h

Show this help message and exit.

-v

Show program’s version number and exit.