This tool average multiple bigWig files based on the number of mapped reads. To average the bigWig files, the genome is partitioned into bins of equal size, then the scores in each bigwig file are computed per bin.These scores are averaged and scaleFactors can be applied before the average.

usage: bigwigAverage -b -o
help: bigwigAverage -h / bigwigAverage --help

Named Arguments

--bigwigs, -b

Bigwig files separated by space.


Set this parameter to multipy the bigwig values by a constant. The format is scaleFactor1:scaleFactor2:scaleFactor3 etc. For example 0.7:1 to scale the first bigwig file by 0.7 while not scaling the second bigwig file

--skipNonCoveredRegions, --skipNAs

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


show program’s version number and exit

--binSize, -bs

Size of the bins, in bases, for the output of the bigwig/bedgraph file. (Default: 50)

--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.

--blackListFileName, -bl

A BED or GTF file containing regions that should be excluded from all analyses. Currently this works by rejecting genomic chunks that happen to overlap an entry. Consequently, for BAM files, if a read partially overlaps a blacklisted region or a fragment spans over it, then the read/fragment might still be considered. Please note that you should adjust the effective genome size, if relevant.

--numberOfProcessors, -p

Number of processors to use. Type “max/2” to use half the maximum number of processors or “max” to use all available processors. (Default: 1)

--verbose, -v

Set to see processing messages.


--outFileName, -o

Output file name.

--outFileFormat, -of

Possible choices: bigwig, bedgraph

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

deepTools Galaxy.

code @ github.