This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to include samples names in assignTaxonomy of DADA2

Dear All, I gave carried out assignTaxonomy for 3 samples using the following command. I would like to know how to include sample names to the resultant file.

taxa <- assignTaxonomy(seqtab.nochim, 
                       "/Users/apple/Desktop/Databases/dada/dada.good.fasta", 
                       multithread=TRUE)

Regards, Dinesh S L

sequencing next-gen gene r
• 2,152 views • link
updated by h.mon h.mon • written by sankadinesh • sankadinesh

1 answer

Hi,

You cannot do it. The taxa object is a taxonomy table that maps the ASVs (Amplicon Sequence Variants) to the respective taxonomy, where each column represents a different taxonomic rank, and each row represents a different ASV. So, no samples here.

What probably you're interested in is how to combine the taxonomy table with the ASV count table (with samples on the rows and the ASVs on the columns) built before. But that is another question, and it depends on your data structure etc.

If you want to analyze this data downstream on phyloseq, there is no need, because dada2 tutorial provides you a description how to do it: https://benjjneb.github.io/dada2/tutorial.html

I hope this helps,

António

• 0 views • link
written by antonioggsousa antonioggsousa

Log in to answer this question.

More posts like this