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bacpop / unitig-counter

Uses cDBG to count unitigs in bacterial populations
GNU Affero General Public License v3.0
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graph output files to GFA #14

Open nwespe opened 3 years ago

nwespe commented 3 years ago

Hi, Thanks for the great tool and for PySEER! I'd like to visualize the cDBG underlying the unitig counts but do not know how to work with the output files created (graph.h5, graph.edges.dbg, and graph.nodes). Is there a program to convert these files to GFA format or another format that would be recognized by Bandage?

johnlees commented 3 years ago

If you run this script it will create a networkx file which you can manipulate, or visualise with cytoscape. (you can safely ignore the 'extend' part)

Unless your cDBG is quite small, it will probably not be possible to visualise the whole thing. Unlike DBGs for assemblies (the typical use for bandage) there are likely to be many edges in your graph. You could try generating an ego graph for a region of interest. If you are interested in GWAS specifically, you could also check out the visualisation module of DBGWAS, which automates this and will create cytoscape visualisations for regions around significant hits.