Open paul-bio-hh opened 3 years ago
Hi @paul-bio-hh, I have a similar issue. I'm considering to sum the counts for each specie (all its OTUs in one). Because in some cases, if I sum all the species' OTUs counts corresponding to a specific genus and sample, the outcome fits in the genus counts' table that our facility also sent. This is tricky because if I calculate the alpha percentages (per sample), this would differ if I don't merge the OTUs with the same specie's annotation, or if I merge them into a single specie (with a new OTU id).
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,
table(tax_table(log.ps)[,"Species"]) 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?