Hello
I have been trying to visualise unassembled overlaps between contigs produced in HGAP.
As suggest, I have run CA_best_edge_to_GML.py and converted the best.edges to a gml file which can be opened in Gephi.
When I open the gml file there are over 4000 nodes and consequently it is impossible to visualise the overlaps between the 3 contigs. I have manually investigated these overlaps and know that the contigs can be merged.
I have never used Gephi before and I assume there is some way of filtering the graph to obtain a meaningful visualisation of overlaps?
Regards
Brian
I have been trying to visualise unassembled overlaps between contigs produced in HGAP.
As suggest, I have run CA_best_edge_to_GML.py and converted the best.edges to a gml file which can be opened in Gephi.
When I open the gml file there are over 4000 nodes and consequently it is impossible to visualise the overlaps between the 3 contigs. I have manually investigated these overlaps and know that the contigs can be merged.
I have never used Gephi before and I assume there is some way of filtering the graph to obtain a meaningful visualisation of overlaps?
Regards
Brian
Comment