Optimization mode#

To launch the algorithm type the following at the command line:

python3 -m optimalTAD run [-h] [--hic HIC [HIC ...]] [--chipseq CHIPSEQ [CHIPSEQ ...]]
                [--np NP] [--resolution RESOLUTION] [--stepsize STEPSIZE]
                [--gamma_max GAMMA_MAX] [--hic_format HIC_FORMAT]
                [--empty_row_imputation] [--truncation] [--log2_hic]
                [--log2_chip] [--zscore_chip]

-h, --help#

Help message

--hic#

Iteratively corrected Hi-C matrices in .hdf5 or .cool format

--chipseq#

Epigenetic data (ChIP-seq in .bedgraph or .bw format)

--np#

Number of processors (=1)

--resolution#

Resolution of Hi-C matrices (=1)

--stepsize#

Step size to increment gamma parameter in Armatus (=0.05)

--gamma_max#

Max value of the gamma parameter (=4)

--hic_format#

Hi-C matrices input format for armatus (=txt.gz)

--empty_row_imputation#

Empty line imputation (=False)

--truncation#

Truncation of a Hi-C-matrix (=False)

--log2_hic#

log2 transformation of Hi-C matrix (=False)

--log2_chip#

log2 transformation of ChIP-seq values (=False)

--zscore_chip#

Z-score transformation of ChIP-seq values(=False)