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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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Importing ASV table and taxonomy #1220

Open Spiderand opened 5 years ago

Spiderand commented 5 years ago

Hey all,

I am new to phyloseq and have a question about loading taxonomy in the package. I have created an ASV table using the dada2 ITS pipeline workflow [https://benjjneb.github.io/dada2/ITS_workflow.html] however, for taxonomy I don't have a table, instead I created an object with a path as such:

unite.ref <- "/Users/macbookpro/thesis-data-2019/sh_general_release_dynamic_02.02.2019.fasta"

Do I have to create a taxonomy table or can I import taxonomy as .fasta? Is there anything else I need to do to properly get my sequences into phyloseq?

Thanks,

Andrew

mikemc commented 5 years ago

Hi Andrew, in a DADA2 workflow, once you process your amplicon data with DADA2, you then need to perform taxonomy assignment, which involves matching the ASVs from your DADA2 results against a database file of sequences with taxonomies already given. You then import the results of the taxonomy assignment into phyloseq. It looks like instead you are asking if you can import the database into phyloseq, without doing the assignment. Take a look at the Taxonomy section at the end of the DADA2 ITS tutorial, and then also read the Taxonomy and Bonus: Handoff to Phyloseq sections of the main DADA2 tutorial.