mergeBedgraph

mergeBedgraph is a tool to merge multiple bedgraph files with multiple replicates.

Usage: mergeBedgraph [options] ...

Content

Required arguments

-f <file_list>

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

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

-m <average_method>

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

Optional arguments

-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.