HI Qiime community,
I am trying to run alpha and beta diversity on y 16S dataset using the core metrics pipeline but ran into an issue while trying to decide what sampling depth because I am trying to divide my 16S dataset into 2 subsets based on taxonomy. For my overall analysis I am looking to analyze the cyanobacterial communities and all non cyanobacteria bacterial communities in my samples. To divide my dataset I used the qiime taxa filter-table plugin to include or exclude cyanobacteria. I would now like to run the core metrics diversity pipeline on those 2 subsets however among the cyanobacteria the sequencing depth varies from about 300 to 50,000 since cyanobacteria are not highly abundant in some samples due to collection methods. I do not want to drop any samples but am worried about using such a low sampling depth of 300.
My question is if there is any way/ would it be valid to run the core metrics on the whole dataset (cyanobacteria+bacteria) to be able to use a higher sampling depth for rarefaction and then filter the rarefied_table.qza by taxonomy into the bacteria and cyanobacteria subsets and then calculate the alpha and beta diversity metrics on the bacteria and cyanobacteria tables to look at the diversity among those 2 communities.
The only other options I could think of would be to just run the core metrics on the feature tables filtered by taxonomy into the cyanobacteria and bacteria groups and just use the low sampling depth resulting in losing a lot of the data from some of the samples or to export the filtered tables and normalize by converting to Relative abundance and running the analysis in some other program such as R. I tried exporting and normalizing the tables (converting to relative abundances) and then importing back into qiime 2 to use the alpha and beta diversity plugins which I saw recommended on other posts but it was returning extra vectors.
I am currently running qiime 2 2018.6 in a virtual box .
Any help would be much appreciated