Los Angeles River
1. Decontaminated and filtered ASV tables
2. List of all the taxa found
Decontamination and Filtering Steps
step 1. Raw ANACAPA files
ANACAPA output ASV table at 70% confidence for 12S, 18S, 16S, PITS, FITS, and CO1.
step 2. Decontaminate the files
Name of the sampling tubes were added to the sequencing id. Samples were decontaminated by eliminating from all the samples the sequences that appeared in the extraction blanks. We keep the sequences that never appeared in the blank. Blank samples columns were then removed.
step 3. Minimum read filtering
Taxa with low read count were filtered out using the filter_taxa function in phyloseq. The minimum total for a taxa was set at 5 read total. filter_taxa(phyloseq_object, function(x) sum(x) > 4, T)