Cyanobacteria - filter out or not?

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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Cyanobacteria - filter out or not? #1417

Open vrbacky opened 3 years ago

vrbacky commented 3 years ago

There are some Cyanobacteria identified in our nasopharyngeal data (about 3% reads, 2% ASVs; Silva v138). What do you recommend to do with such ASVs? Should I filter them out? Our project is not cyanobacteria/chloroplast related. It is interested in microbial communities only.

Thanks

Filip

fconstancias commented 3 years ago

Hi Filip,

If you have included negative controls in your librayry, you could try decontam R package to try to filter out potential contaminants ASV which might come from extraction kit, or molecular biology related stuff.

What are the full taxonomic assignements of those ASVs? I would blast the ASV sequences?