Configuration file

Below, we provide a template of the configutation file required for optimalTAD. While this template is needed for both ‘optimization’ and ‘visualization’ modes, [visualization] section is targeted for ‘visualization’ mode and doesn’t affect TAD set optimization process.

# .ini basic configuration file

[basic]
mode = run

[run]
hic = ./testdata/LacZ1_2L.hdf5
chipseq = ./testdata/LacZ1_2L.bedgraph
np = 3
resolution = 20000
stepsize = 0.05
gamma_max = 4
hic_format = txt.gz
truncation = True
log2_hic = True
log2_chip = True
zscore_chip = True
empty_row_imputation = False

[chromosomes]
set_chromosomes = chr2L # should be separated by commas

[hic]
shrinkage_min = 0.5
shrinkage_max = 1024
balance = True

[stair]
index_min = -4
index_max = 5
acetyl_min = -3
acetyl_max = 5

[output]
path_to_amplitude_figure = output/figures/StairAmplitude
path_to_amplitude_file = output/amplitudes.csv
path_to_best_stair_data = output/stair.csv
path_to_stair_data = output/all_stairs.csv
path_to_best_stair_figure = output/figures/BestStairs
figure_postfix = png
figure_dpi = 300

[visualization]
samplename = LacZ_1
region = chr2L:0-6,000,000
path_to_chip = ./testdata/LacZ1_2L.bedgraph
rnaseq = False
fontsize = 12
nticks = 5
cmap = coolwarm
hic_text = Hi-C
chip_text = H3
rnaseq_text = RNA-Seq
vline_linewidth = 1
vline_linestyle = dashed
tad_linewidth = 1.2
tad_linestyle = --
filename = output/figures/TADandChIPseq.png
dpi = 300