HicPlotTADs Hi-C contacts not being plotted

[aminakur]

I am trying to plot TADs I called on a Hi-C matrix with resolution 1kb. But no contacts are being plotted on the map. This is my command: hicPlotTADs --tracks tracks.ini --region chr01:6800000-8500000 -o HiCExplorer_TADs_1kb.png tracks.ini file:

[x-axis]
fontsize=10

[hic]
file = /scratch/ak8725/az_mrg/az_mrg.mcool::resolutions/1000
title = 1kb - Sun et al., 2020
colormap = Spectral_r
depth = 40000
min_value = 1
max_value = 80
transform = log1p
file_type = hic_matrix
show_masked_bins = false

[tads]
file = /scratch/ak8725/az_mrg/hicFindTADs/hicFindTADs2_out/az_mrg2_domains.bed
file_type = domains
border_color = black
color = none
overlay_previous = share-y

[spacer]
height = 0.1

[hic]
file = /scratch/ak8725/az_mrg/az1kb.cool
title = 1kb
colormap = Spectral_r
depth = 400000
min_value = 1
max_value = 80
transform = log1p
file_type = hic_matrix
show_masked_bins = false

[tads]
file = /scratch/ak8725/az_mrg/hicFindTADs/hicFindTADs3_out/az_mrg3_domains.bed
file_type = domains
border_color = black
color = none
overlay_previous = share-y

The output is weird

I don't think this is due to the sparcity of the matrix, this is a screenshot from HiGlass of the same region with 1kb resolution:

I am getting the same output with 5kb resolution:

[lldelisle]

Hi, I think the problem is with the min_value and max_value. Could you try without setting them, please?

[aminakur]

Better, but still not great.

Is this because of the missing data? Are there other parameters I can tweak?