(even w/ data from blanks, it can be tricky. e.g. you may have contaminant Burk in blanks & real Burk in samples. also possibility of cross-contamination from sample⇾blank. but it’s better than not having any data at all! Btw, I recommend decontam: ht
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RT @melikedonertas: 3-decontam is an in-silico tool to identify contaminants in marker-gene and metagenomics data. it doesn't rely on exter…
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3-decontam is an in-silico tool to identify contaminants in marker-gene and metagenomics data. it doesn't rely on external data of contaminants or risk low-abundance true ASVs across samples. it requires information on total DNA conct or seq'd - controls.
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@surt_lab @DrHeathHeckman @MarcoEMechan esp if the originating samples are expected to be low microbial biomass, you can use any sequences from negative control to decontam, as in: https://t.co/ppukTy5Cyi and similar approaches working in the phyllosphere