Identifies enriched contacts by computing a observe vs. expected or a z-score matrix

usage: hicFindEnrichedContacts --matrix MATRIX --outFileName OUTFILENAME
                               --method {z-score,obs/exp} [--perchr]
                               [--skipDiagonal] [--maxDepth MAXDEPTH] [--help]

Required arguments

–matrix, -m Input matrix.
–outFileName, -o
 File name to save the resulting matrix.

Possible choices: z-score, obs/exp

Method to transform the matrix values.

Optional arguments


Default is to fit distributions per each distance. Setting this option will fit distributions per distance per chromosome.

Default: False

–skipDiagonal, -s

If set, diagonal counts are not included.

Default: False

–maxDepth Depth (in base pairs) up to which the computations will be carried out. A depth of 10.0000 bp means that any computations involving bins that are over 10kbp apart are not considered.
–version show program’s version number and exit