Shared OTUs profiling

Other Bioinformatics Tools
1

Dear all,

I have created a biom for my dataset which consists 9 samples. I was able to obtain the number of otus shared among each pair of sample using shared_phylotypes.py. However, I would like to generate a profile which would contain number of shared otus among 3 specific sample sets or 4 sample sets and number of OTUs common in all the 9 samples. Can someone guide me on how I could get to this.

Any help is highly appreciated. Thanks in advance.

  • Vijay
2

Hi! I am not sure I understood you, but I suppose your solution is to filter your table and create a new one which contains only the samples of your wish, then repeat core features analysis with this table as well. In the tutorials there is one how to filter a table