Is it possible to create a table with the taxonomic composition of a sample, that would have ALL the taxonomic levels? (i.e. containing the sample IDS and the sequence counts for all the toxonomic level all in the same table)
Now I seem to be forced to choose just one level and collapse, but I would like to bring them all together.
Is there a way to do it, or would it possible to add this function?
Right now the only way I see is generating the 6 csv files, concatenate them, and then delete the following lines (headers) that would be duplicated.
If you don't mind my asking, what are you planning on using that for? Unless I'm misunderstanding, you'll end up with redundant observations because of the hierarchy in a taxonomy. But I suppose that's not necessarily a problem so long as you are aware of it.
In principle you should be able to use qiime feature-table merge a couple of times to accomplish this.
I don’t mind the question at all. I plan to test different approach of machine learning using OTU count. I want to test the model with separate tables for each taxonomic levels, but I also want to test the model using all the OTU counts for all the taxonomic levels altogether, as there might be an influence of some bacteria in higher taxonomic level affecting the presence of other groups in lower taxonomic levels. Shortly, that’s about it.
So I will try your suggestion with the merge command and see if it works, thank you very much again!