how to proceed after dada2 output

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:

  1. Filter the feature table count based on tissue and region
  2. 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.

Kind Regards

Hi! I am doing the same by filtering and collapsing feature table without redoing trees

Hi @timanix,

Thanks, but if I need to import data into phyloseq, it ask for tree, in that case, should I use tree which generated for whole data to import in phyloseq?


Hi @Yogesh_Gupta,
As long as no new samples are added you can use the same tree from the complete dataset on your subset table, as @timanix mentioned. But if you would still like to re-create your tree with specific samples only, you can simply filter your rep-seqs with filter-seqs in whatever way you need and re-create a tree based on the new file. The same concept occurs in phyloseq as well. As for using different taxonomic levels assignment you can use the taxa collapse function in Qiime2 to simply create a new feature-table at the desired level or tax_glom in phyloseq which acts similarly to collapse.


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