This tool compares two bigWig files based on the number of mapped reads. To compare the bigWig files, the genome is partitioned into bins of equal size, then the number of reads found in each BAM file are counted per bin and finally a summary value is reported. This value can be the ratio of the number of readsper bin, the log2 of the ratio, the sum or the difference.

usage: bigwigCompare [-h] [--version] [--binSize INT bp]
                     [--region CHR:START:END] [--numberOfProcessors INT]
                     [--verbose] --outFileName FILENAME
                     [--outFileFormat {bigwig,bedgraph}] --bigwig1 Bigwig file
                     --bigwig2 Bigwig file [--scaleFactors SCALEFACTORS]
                     [--pseudocount PSEUDOCOUNT]
                     [--ratio {log2,ratio,subtract,add,reciprocal_ratio}]
optional arguments
--bigwig1, -b1 Bigwig file 1. Usually the file for the treatment.
--bigwig2, -b2 Bigwig file 2. Usually the file for the control.
--scaleFactors Set this parameter to multipy the bigwig values by a constant. The format is scaleFactor1:scaleFactor2. For example 0.7:1 to scale the first bigwig file by 0.7 while not scaling the second bigwig file
 small number to avoid x/0. Only useful when ratio = log2 or ratio

The default is to compute the log2(ratio) between the two samples. The reciprocal ratio returns the the negative of the inverse of the ratio if the ratio is less than 0. The resulting values are interpreted as negative fold changes. Other possible operations are : simple ratio, subtraction, sum

Possible choices: log2, ratio, subtract, add, reciprocal_ratio

--skipNonCoveredRegions=False, --skipNAs=False
 This parameter determines if non-covered regions (regions without a score) in the bigWig files should be skipped. The default is to treat those regions as having a value of zero. The decision to skip non-covered regions depends on the interpretation of the data. Non-covered regions in a bigWig file may represent repetitive regions that should be skipped. Alternatively, the interpretation of non-covered regions as zeros may be wrong and this option should be used
Optional arguments
--version show program’s version number and exit
--binSize=50, -bs=50
 Size of the bins, in bases, for the output of the bigwig/bedgraph file.
--region, -r Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example –region chr10 or –region chr10:456700:891000.
--numberOfProcessors=max/2, -p=max/2
 Number of processors to use. Type “max/2” to use half the maximum number of processors or “max” to use all available processors.
--verbose=False, -v=False
 Set to see processing messages.
--outFileName, -o
 Output file name.
--outFileFormat=bigwig, -of=bigwig

Output file type. Either “bigwig” or “bedgraph”.

Possible choices: bigwig, bedgraph

deepTools Galaxy. code @ github.