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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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table(tax_table(log.ps)[,"Species"]) questions. #1433

Open paul-bio-hh opened 3 years ago

paul-bio-hh commented 3 years ago

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"]) image 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?

elenu commented 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).