I have imported data from qiime2.
And this is the code that I used to import qiime to phyloseq
ps.ng.tax <- read_phyloseq(otu.file = “table_taxonomyV2.biom”,
taxonomy.file = NULL,
metadata.file = “metadata-renew.csv”,
type = “biom”)
I have question. When I look up the tax table in species level,
For example I have 4 Campanella. I thought this means 4 differenct ASVs are annotated with one Campanella. right?
However my coworker told me that only 1 has to be written instead of 4. He is saying identical species have to be collapsed.
So the question is When I import feature table(=otu table) from qiime2, should I collapse and then import to phyloseq?
Or is it okay to use table from DADA2?
Can you tell me the suggestion?