hicHyperoptDetectLoops (version 3.7.2+galaxy0)

Matrix to compute on:

Protein peak file in bed format:

The protein file to validate the detected loops.

Maximum number of loops:

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

Resolution of the matrix:

The matrix resolution of the Hi-C interaction matrix.

Add, remove, or keep the chr-prefix of the loop/TAD data:

Hyperopt runs:

The number of iterations hyperopt uses to search for a result

Hyperopt parameter optimization loop detection

Compute with a protein peak data file (bed format) optimal parameters for the loop calling. Useful proteins are e.g. CTCF or cohesin.

Usage

A command line example is available below (easily matchable in Galaxy using each field information):

̀`$ hicHyperoptDetectLoops -m matrix.cool -o hyperopt_result.txt --maximumNumberOfLoops 10000 --resolution 10000 --runs 100`

For more information about HiCExplorer please consider our documentation on readthedocs.io.