There are no sequence labels on the HiC contact map

[GallVp]

Description of the bug

• Add sequence labels to the contact map.

Command used and terminal output

No response

Relevant files

No response

System information

plant-food-research-open/assemblyqc 2.1.1

[GallVp]

The pipeline uses 3d-dna visualize/run-assembly-visualizer.sh to convert a links file into a hic file. The script removes assembly sequence labels and replaces them with a single label: assembly. Thus, the only label visible on the HiC contact map is assembly.

The pipeline also produces a .assembly and a .bedpe file. The .bedpe file is added to the HiC contact map as annotation in the html report. Using this annotation, the contact map shows blue rectangles on the map to indicate the scaffold boundaries. But it does not show the labels. So the current solution is to show a table below the HiC contact map which lists the sequence labels.