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benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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Filter plants contigs after dada2 ITS workflow #1797

Closed laisoemis closed 1 year ago

laisoemis commented 1 year ago

I'm working with metabarcoding of fungi associated with plant tissues. After processing the data through the DADA2 ITS Pipeline Workflow (1.8) I realized through the taxonomy table that there is a large amount of DNA from the plants themselves. I plan to continue with diversity analyzes via the phyloseq and vegan package, but first I need to filter out the plant contigs. How could I do this?

gzahn commented 1 year ago

You can filter them out in phyloseq(keeping only fungi), using: phyloseq::subset_taxa(ps, Kingdom == "k__Fungi")