Hi everyone,
First, thank you very much for developing and maintaining Minigraph-Cactus and the ODGI-based visualization workflow for pangenome graphs. These tools have been very helpful in exploring our fungal pangenome graph at the chromosome scale.
I generated chromosome-level ODGI visualizations from a Minigraph-Cactus run using the --odgi option. While inspecting the plots, I had two questions and would be very grateful for your guidance.
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In some chromosome visualizations, the lower part of the plot contains very dense black lines, whereas in other chromosomes this part is much less dense. My understanding is that this lower panel reflects graph topology/connectivity, but I wanted to confirm what these black lines specifically represent in the ODGI view. Are they showing node-to-node connections, graph edges after layout, or another aspect of graph structure? Also, is it reasonable to interpret higher density in this region as reflecting greater local graph complexity or structural variation among assemblies?
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In the upper path tracks across the 13 assemblies, some regions appear to show path absence/gaps in certain assemblies, while other assemblies clearly traverse those same regions. I would like to zoom into such regions and generate finer-scale figures that clearly show the local variation in the pangenome graph.
Could you please suggest the best way to do this? In particular, I would appreciate recommendations on:
- how to identify and extract a local region/subgraph of interest from the chromosome-scale pangenome graph,
- how to zoom into that region at a finer scale,
- and which ODGI or related commands/workflows are most suitable for generating clean figures for poster or presentation use.
Thank you again for developing these tools and for any advice you can share.
Best regards,
Sumit
Hi everyone,
First, thank you very much for developing and maintaining Minigraph-Cactus and the ODGI-based visualization workflow for pangenome graphs. These tools have been very helpful in exploring our fungal pangenome graph at the chromosome scale.
I generated chromosome-level ODGI visualizations from a Minigraph-Cactus run using the
--odgioption. While inspecting the plots, I had two questions and would be very grateful for your guidance.In some chromosome visualizations, the lower part of the plot contains very dense black lines, whereas in other chromosomes this part is much less dense. My understanding is that this lower panel reflects graph topology/connectivity, but I wanted to confirm what these black lines specifically represent in the ODGI view. Are they showing node-to-node connections, graph edges after layout, or another aspect of graph structure? Also, is it reasonable to interpret higher density in this region as reflecting greater local graph complexity or structural variation among assemblies?
In the upper path tracks across the 13 assemblies, some regions appear to show path absence/gaps in certain assemblies, while other assemblies clearly traverse those same regions. I would like to zoom into such regions and generate finer-scale figures that clearly show the local variation in the pangenome graph.
Could you please suggest the best way to do this? In particular, I would appreciate recommendations on:
Thank you again for developing these tools and for any advice you can share.
Best regards,
Sumit