mergeBigwig

mergeBigwig is a tool to merge multiple bigwig files with multiple replicates.

Usage:   mergeBigwig [options] ...
             1) pre-existing window bins
             mergeBigwig -f <file_list> -m <average_method> -n <windows_name>
             2) building window bins for hg38/hg19/mm10
             mergeBigwig -f <file_list> -m <average_method> -b <bin_size> -s <species> [-n <windows_name>]
             3) building window bins for custom species
             mergeBigwig -f <file_list> -m <average_method> -b <bin_size> -g <genomesizes> -n <windows_name> [-B <blackList>]

Content

Required arguments

-f <file_list>

Tab-delimited file listing input/output pairs [Default: None]. Example:

/PATH/TO/A_rep1.H3K36me3.bw   /PATH/TO/A.H3K36me3.bw
/PATH/TO/A_rep2.H3K36me3.bw   /PATH/TO/A.H3K36me3.bw
/PATH/TO/B_rep1.H3K36me3.bw   /PATH/TO/B.H3K36me3.bw
/PATH/TO/B_rep2.H3K36me3.bw   /PATH/TO/B.H3K36me3.bw
/PATH/TO/B_rep1.H3K9me3.bw    /PATH/TO/A.H3K9me3.bw
/PATH/TO/B_rep2.H3K9me3.bw    /PATH/TO/A.H3K9me3.bw
...

-m <average_method>

Merging method for signal values. Support choices: mean, median. [Default: mean]

-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
...

-c <cor_method>

Correlation method for quality control. Support choices: spearman, pearson. [Default: pearson]

-z

By setting this option, genomic regions that have zero or missing (nan) values in all samples are excluded. [Default: false]

-l <cutoff_cor>

Minimum correlation threshold for QC warnings [Default: 0.1]

-q

Disable QC warnings. [Default: false]

-p <nthreads>

Number of parallel processes. [Default: 4]

-h

Show this help message and exit.

-v

Show program’s version number and exit.