GianBen

Hey @benjjneb Thanks a lot and yeah, that's very interesting. I am also not using `phyloseq` very often, but I did for this dataset since involved other collaborators that were...

Sure, let me double check the files and I will write you an email.

Thank you for explanation, now makes sense. I had similar results using the `--characterize` option. All the contigs were written into the `.plasmid.fasta` file while the `.chromosome.fasta` file was empty....

I have tried to comapre the two outputs with (bottom, secon cat) and without (top, first cat) the `--characterize` option and I am not sure how to interpret the result....

Hey @oschwengers, thanks for the explanation, very useful. I am still confused, though, about what the `# Plasmid Hits` field means in the `--characterize` mode of platon. I have several...

Hello @oschwengers , Thanks for the explanation. So this means that the characterization may be not 100% correct due to the reasons you mention above, while the default mode it...

ok @oschwengers, will look into the manual. I think I did not specified `accuracy` mode when I run it. Thanks a lot, Gian

Hello @thomasp85 and thanks for your reply, I think the problem is more related to a network layout than other things, not sure how to solve it though. It could...

I am not totally sure though that is the only issue, if you look at this graph you can see FOTU_115 is connected to FOTU_201, but that connection does not...

Thanks for the prompt reply @thomasp85, I believe you. I am not saying it is wrong, I am just trying to find a solution as I want to really use...