genomeWindows

genomeWindows is a tool to segment the genome into equally sized and contiguous bin. The output files are used for downstream S3V2 normalization.

Usage: genomeWindows [options] -b <bin_size> -s <species> [-n <windows_name>]
       genomeWindows [options] -b <bin_size> -g <genomesizes> -n <windows_name> [-B <blackList>]

Content

Required arguments

-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
...

-n <windows_name>

Required if -s is unspecified. A unique name to identify the generated window bins for downstream processing [Default: None].

Optional arguments

-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
...

-l

List available pre-built window bins and their metadata.

-h

Show help message and exit.

-v

Show version number and exit.