The gamtools bias tool is used to calculate the bias that could be attributed to a particular genomic feature. Given a bedgraph file with a value for each genomic window, the tool generates ten bins, each containing an equal number of genomic windows, based on the feature. For example, if the bedgraph file contains restriction site density, bin one would contain the genomic windows with the 10% lowest site density and bin ten would contain the 10 highest. It then calculates the mean interaction frequency between windows in each possible combination of bins, normalised for linear genomic distance.

Usage and option summary


gamtools bias [OPTIONS] -f <FEATURE_FILE> -o <OUTPUT_PATH> -m <MATRIX> [<MATRIX> ...]

Required parameters:

Option Description
-f, –feature-path Path to input bedgraph containing one value per genomic window.
-m, –matrix-paths Path to one or more interaction matrices to use for calculating biases.
-o, –output-path Output bias matrix file. Path to use for saving the result of the bias calculation.