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chicViewpointBackgroundModel (version 3.6+galaxy1)
Bed file contains all reference points which should be used to build the background model.
Average the contacts of n bins via a sliding window approach.
Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.
Set this parameter if you want truncate zeros to fight over dispersion.

Compute a background model for cHi-C data analysis

chicViewpointBackgroundModel computes for all given samples with all reference points a background model. For all relative distances to a reference point a negative binomial distribution is fitted. Moreover, for each relative distance to a reference point the average value for this location is computed. Both background models are used, the first one for p-value and significance computation, the second one to filter out interactions with a less x-fold over mean.

The background distributions are fixed at --fixateRange i.e. all distances lower / higher than this value use the fixed background distribution.

For more information about HiCExplorer please consider our documentation on