# bigwigCompare¶

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]