Los Angeles River

• Intro
• Overview
• Organisms Tree
• Sampling Types
• Area Diversity
• Plants and Animals
• Detection Frequency
• Appendix

Appendix

Files

1. Decontaminated and filtered ASV tables

LA_river_CO1_ASV_sum_by_taxonomy_70_dc_ed_min5.csv

LA_river_FITS_ASV_sum_by_taxonomy_70_dc_ed_min5.csv

LA_river_PITS_ASV_sum_by_taxonomy_70_dc_ed_min5.csv

LA_river_X12S_ASV_sum_by_taxonomy_70_dc_ed_min5.csv

LA_river_X16S_ASV_sum_by_taxonomy_70_dc_ed_min5.csv

LA_river_X18S_ASV_sum_by_taxonomy_70_dc_ed_min5.csv

2. List of all the taxa found

taxa_list_min5.csv

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)