There is no data for the region considered on the matrix.

[ec233133]

I am trying to plot TADs using the HiCPlotTADs tool , but I keep receiving the same error.

INFO:pygenometracks.tracksClass:plotting 1. [x-axis]
INFO:pygenometracks.tracksClass:plotting 2. [hic matrix]
WARNING:pygenometracks.tracks.GenomeTrack:*Warning*
There is no data for the region considered on the matrix. This will generate an empty track!!

In the provided .ini file, I did use the H5 file produced by Hicexplorer. Why is the matrix still empty?

The ini files are as follows:

[x-axis]
where = top

[hic matrix]
file = Mock_corrected_KR.h5
title = hic_data
# depth is the maximum distance plotted in bp. In Hi-C tracks
# the height of the track is calculated based on the depth such
# that the matrix does not look deformed
depth = 125000
transform = log1p
file_type = hic_matrix

[tads]
file = Mock_hic_corrected_domains.bed
display = triangles
border_color = black
color = none
# the tads are overlay over the hic-matrix
# the share-y options sets the y-axis to be shared
# between the Hi-C matrix and the TADs.
overlay_previous = share-y

[lldelisle]

Hi, Sorry for the late reply. Your depth seems super small, can you try to increase it?

[ec233133]

Where can I add an assertion point to check the instant shut down error? Many thanks

[ec233133]

Hi, @lldelisle Thank you for your advice, and I was able to successfully make the deep changes later! Thanks again.

[x-axis]
where = top

[hic matrix]
file = 1020corrected_KR_Mock_nb10.h5
title = Hi-C data
# depth is the maximum distance plotted in bp. In Hi-C tracks
# the height of the track is calculated based on the depth such
# that the matrix does not look deformed
depth = 3000000
transform = log1p
file_type = hic_matrix 

However, I encountered another issue. After placing the file in the domains.bed, the program crashed again.

pyGenomeTracks --tracks hic_track.ini -o Mock_chr1_hic_track.png --region chr1:10000000-40000000 --dpi 300
INFO:pygenometracks.tracksClass:initialize 1. [x-axis]
INFO:pygenometracks.tracksClass:initialize 2. [hic matrix]
強制結束

The details of the "hic_track.ini" file are as follows:

[x-axis]
where = top

[hic matrix]
file = 1020corrected_KR_Mock_nb10.h5
title = Hi-C data
# depth is the maximum distance plotted in bp. In Hi-C tracks
# the height of the track is calculated based on the depth such
# that the matrix does not look deformed
depth = 3000000
transform = log1p
file_type = hic_matrix

[tads]
file = hicFindTADs_on_data_317__TAD_domains.bed
display = triangles
border_color = black
color = none
# the tads are overlay over the hic-matrix
# the share-y options sets the y-axis to be shared
# between the Hi-C matrix and the TADs.
overlay_previous = share-y

I believe there might be an issue with HicFindTADs @@, but I'm not sure how to resolve it.

[lldelisle]

Sorry, I cannot see the error. Can you show me the full log please?

[ec233133]

Hi, @lldelisle I can generate images by processing the files separately, but when combined, it results in a forced termination. Could this be because I provided incorrect parameters in HicFindTADs initially?

[lldelisle]

I am not sure I understand. You mean that if you display the bed file by itself you get an image and if you display the h5 by itself you also get an image but if you display both it crashes? Can you try to plot without overlay, to see how it behaves? Thanks

[ec233133]

hi, @lldelisle I'll give it a try! Very grateful for your assistance.