Microbial network in Cytoscape from NGS data

Question

[stuskova.katerina]

Hi, I am a complete beginner with NGS and network analysis. I have a data from NGS in excel table. First column is genus of fungi and next columns are genes (SR2, SF2, MF2...a total of 23 genes) with numbers for some genera. I need create network some like this figure 3 (https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-0787-2) from my data.

How do I process data for processing in Cytoscape?

I'm completely desperate, I've never worked with this in my life ...

I will be happy for any response, thank you

Answer 1

[Kevin Blighe]

I think that we are somewhat limited in how we can help, in this regard. The best place for you to start is the Cytoscape manual pages to learn about the different data input formats:

• http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html#

Perhaps you should first figure out what the network should represent? Once you know that, it is useful to know that virtually all network visualisation programs will take data of the generic form:

vertex1 --> vertex2
vertex1 --> vertex3
vertex1 --> vertex6
vertex2 --> vertex3
... ...

This can simply be a 2-column file.

Kevin