hicHyperoptDetectLoopsHiCCUPS¶
usage: hicHyperoptDetectLoopsHiCCUPS --matrix MATRIX --proteinFile PROTEINFILE
--maximumNumberOfLoops
MAXIMUMNUMBEROFLOOPS --juicerPath
JUICERPATH
[--outputFileName OUTPUTFILENAME]
[--resolution RESOLUTION]
[--chrPrefixLoops {None,add,remove}]
[--runs RUNS] [--threads THREADS]
--normalization NORMALIZATION [--cpu]
[--restricted] [--help] [--version]
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.
- --juicerPath, -j
path to juicer.jar
- --outputFileName, -o
File names for the result of the optimization (Default: “hyperoptHiCCUPS_result.txt”).
Default: “hyperoptHiCCUPS_result.txt”
Optional arguments¶
- --resolution, -r
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.
- --runs
Number of runs of hyperopt.
Default: 100
- --threads, -t
Number of threads (uses the python multiprocessing module) (Default: 4).
Default: 4
- --normalization, -k
Normalization table name
- --cpu
use the CPU version
Default: False
- --restricted
If the GPU version is used, search only within 8 MB.
Default: False
- --version
show program’s version number and exit