Hello
I have a question on qiime 2 core-features. I know you can look for features that are shared between groups within some percentage using core features. Is there a way to look at unique features? I have two seasonal treatments (summer and spring). I am interested in a)the shared OTUs table-i can use core features for this and b)OTUs that are unique to only summer and spring (not shared)-i am not sure how to obtain this. Is there a way to obtain the OTU table for unique features in qiime 2? Any assistance will be highly appreciated
Hi!
I did the same thing you are describing by obtaining core features with Qiime2.
After it, you can manually copy and paste core features at chosen percentage to make a Venn diagrams using online tools Venny or interactivenn to get unique and shared features (from both sources lists of unique and shared features may be obtained by directly copying from the website or by downloading a diagram as a .txt file). I did is like this at the first time, but since I wanted to get reproducible scripts, later I used list intersections in Python to obtain the lists of unique and shared features.
1 Like
Hi!
Thank you very much for the reply. I was able to make venn diagrams using the OTU list but i am also interested in the OTU abundance list from shared and unique OTUs. I want to do some statistics on the shared and unique OTU relative abundance data. I know i can do it manually, but i wonder if i can get the OTU list with relative abundance data by running a script in qiime 2?
I am not aware of such function in Qiime2, but you can use the list of unique or shared features to filter the biom tables and obtain abundances as well
I will give it a try, thank you very much for your assistance.
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.