chicViewpointBackgroundModel (version 3.7.2+galaxy0)

Matricies to compute on:

Reference points:

Bed file contains all reference points which should be used to build the background model.

Average contacts window size:

Average the contacts of n bins via a sliding window approach.

Clip background distance:

Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.

Truncate zeros:

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 readthedocs.io