usage: hicHyperoptDetectLoops --matrix MATRIX --proteinFile PROTEINFILE
                              --maximumNumberOfLoops MAXIMUMNUMBEROFLOOPS
                              [--outputFileName OUTPUTFILENAME]
                              [--resolution RESOLUTION]
                              [--chrPrefixLoops {None,add,remove}]
                              [--threads THREADS] [--runs RUNS] [--help]

Required arguments

--matrix, -m

The matrix to compute the loops on.

--proteinFile, -p

The protein file to validate the detected loops

--maximumNumberOfLoops, -ml

The maximum number of loops that should be used for optimization computation.

--outputFileName, -o

File names for the result of the optimization (Default: “hyperopt_result.txt”).

Default: “hyperopt_result.txt”

Optional arguments

--resolution, -re

Resolution of matrix (Default: 10000).

Default: 10000

--chrPrefixLoops, -cl

Possible choices: None, add, remove

Adding / removing / do nothing a ‘chr’-prefix to chromosome name of the loops.

--threads, -t

Number of threads (uses the python multiprocessing module) (Default: 4).

Default: 4

--runs, -r

Number of runs of hyperopt (Default: 100).

Default: 100


show program’s version number and exit