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:
Hi,
I ran DADA2 on my 3 datasets, then I got 3 "ps" phyloseq objetcs.
I have the absolute abundaces for these 3 datasets. The thing I need is to convert the ASV sequences by "names" , and to keep the same names between the 3 datasets (to do some comparisons).
I have my 3 ps objects, from which I cleaned the "mitochondrial" and "chloroplastic" ASVs and filtered ASVs with low abundance < 2. I only show for one dataset what I did :
> ps.clean.p0.pool1
phyloseq-class experiment-level object
otu_table() OTU Table: [ 436 taxa and 79 samples ]
sample_data() Sample Data: [ 79 samples by 12 sample variables ]
tax_table() Taxonomy Table: [ 436 taxa by 6 taxonomic ranks ]
Then, I converted the DNA sequences of the ASVs by names :
ASV1" will not correspond to the same DNA sequence between the 3 datasets. How to get the same "ASV names" for the same sequences between the datasets?
Hi, I ran DADA2 on my 3 datasets, then I got 3 "ps" phyloseq objetcs. I have the absolute abundaces for these 3 datasets. The thing I need is to convert the ASV sequences by "names" , and to keep the same names between the 3 datasets (to do some comparisons).
I have my 3 ps objects, from which I cleaned the "mitochondrial" and "chloroplastic" ASVs and filtered ASVs with low abundance < 2. I only show for one dataset what I did :
Then, I converted the DNA sequences of the ASVs by names :
ASV1" will not correspond to the same DNA sequence between the 3 datasets. How to get the same "ASV names" for the same sequences between the datasets?
Best