I run all sample together which belongs to 3 tissue (root, soil, leaf) and 2 different geographic regions (HRPR and LLRP). but now I want to do two things:
- Filter the feature table count based on tissue and region
- to repeat the analysis (Feature count, phylogenetic tree, alpha and beta diversity) at multiple taxonomic level: Phyla, class, order, species, genes
I just want to know can I use the same rep-seqs.qza which is generated during whole data analysis in dada2 to do phylogenetic analysis separately for all filtered sample at the different taxonomic level or should I use the unrooted-tree.qza tree which is generated for whole data analysis to do alpha and beta diversity analysis on filtered samples.