HGAP graph visualisation

[coldturkey]

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

[rhall]

Which Layout option are you using. With 4000 nodes, YifanHu's Multilevel algorithm should work to give you a global view of the data, indicting if the assembly is circular / has bubbles / ambiguous overlaps e.g. a graph for an assembly of 9 fosmids, 5 are clearly assembled into circles, the remaining 4 have an overlap ambiguity and some local complexity.
Richard.

[coldturkey]

Hi Riachard,

I tried Yifan Hu's Multilevel last night and it produced the desired output.

Thank you

Brian

[AndrewRGross]

I came here looking for help visualizing a comparison between communities based on shared OTUs. I haven't quite gotten it, but I've gotten closer by downloading plugins that provide more layout calculators. Its under "tools>plugins".