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bigwigCompare (version 3.5.4+galaxy0)
The default is to output the log2ratio between the two samples. The reciprocal ratio returns the negative of the inverse of the ratio if the ratio is less than 0. The resulting values are interpreted as negative fold changes. To output the scaled values from the first or second bigWig file, select 'first' or 'second'.
Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space.
This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000".

What it does

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 scores (e.g., number of reads) found in each bigWig file are counted for such bins and, finally, a summary value is reported. This value can be the ratio of the number of reads per bin, the log2 of the ratio, the sum or the difference.

Note that you can actually produce a human-readable bedGraph format instead of the compressed bigWig format if you're interested in having a look at the values yourself.


For more information on the tools, please visit our help site.

For support or questions please post to Biostars. For bug reports and feature requests please open an issue on github.

This tool is developed by the Bioinformatics and Deep-Sequencing Unit at the Max Planck Institute for Immunobiology and Epigenetics.