Hello all, is there a command to get the genera core? I have about 300 genera (/unclassified groups) and i am looking to see which genera are prevalent in all samples above a threshold. I tried to create a custom “shared file” with the information i have, and i am going to give it a try. if anyone has some tips, it would be helpful.
phylotype will take your taxonomy file and count table to create a shared file based of taxonomic groupings. It can be done for any taxonomic ranking (phylum -> genus) in your taxonomy file.
Thanks for your reply. I am not looking to perform a phylotype approach. Here is more on what i did.
I did an OTU approach, and then i created a “database” from my shared and taxonomy files …etc. This allowed me to examine my OTUs abundance and also allowed my to sum up my OTUs belonging to the same genus to examine genera abundances as well. To avoid low classification at genus level, i renamed all the “g_unclassfide” to reflect its closest classified parent. My genera or (groups at genus level) looks like this: Butyribirio, Fibrobacter, u_nclassified Bacteroidales_, etc. The groups i created comprises all the sequences and now what i am trying to do is to calculate the core microbiome at “genus” level.
I can sort the file and eye-ball it and i can certainly define at least 10 groups that are prevalent and present in across all samples, but i am trying to so this with selected treatments etc …
The only way i am thinking is to create a custom shared files where my outs are my genera and numOtus are the number of my genera etc…
any thoughts? (I’ve seen this done with a paper that used Qiime)