Open aminakur opened 1 year ago
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:
hicPlotTADs --tracks tracks.ini --region chr01:6800000-8500000 -o HiCExplorer_TADs_1kb.png
[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:
Hi, I think the problem is with the min_value and max_value. Could you try without setting them, please?
Better, but still not great.
Is this because of the missing data? Are there other parameters I can tweak?
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: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: