hicFindEnrichedContacts

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

usage: hicFindEnrichedContacts --outFileName OUTFILENAME --method
                               {z-score,obs/exp} [--perchr] [--skipDiagonal]
                               [--depth DEPTH] [--help] [--version]

Required arguments

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

Possible choices: z-score, obs/exp

Method to transform the matrix values.

Optional arguments

–perchr

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

–depth 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