The bioBakery help forum

Core microbiome species

Hi @fbeghini
I want to find out the core microbial species from the 7 groups of the samples that I have. How do I make venn diagramm from the metaphlan3 merged abundance table? Thera are tools but for that I need biom format table which I am not able to make.

Saraswati Awasthi

There are plenty of packages for creating venn diagrams from vectors (e.g. R VennDiagram). If you are using a package that requires a BIOM file as input, MetaPhlAn can produce a BIOM output by using --biom_output_file

Do I have to run the whole analysis again to obtain the biom format or I can obtain it from the bowtie 2 output files?

No need to re run everything, you can use the bowtie2out as input to generate the BIOM file.