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aeroDADA2

This repository is a submodule. It contains asvs, sequences, and metadata for 16S amplicon data collected from C-20A science flights in the troposphere and lower stratosphere. The original sequences are publicly available on NASA GeneLab: https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-170/

Files

  • README.md: This file!
  • aeRo.R: R script implementation of DADA2 pipeline
  • aeRo.Rproj: corresponding R studio project
  • asv_table.csv: ASV table with tabulated ASV counts corresponding to each sampling sequence
  • sample_data.csv: Metadata for each sampling sequence.
    • Sample.Name: Name of sample
    • Material Type: Extracted DNA for all samples
    • Sample.Description: Qualitative comments on sampling, flight path, negative control, etc.
    • Organism: Metagenomic data for all samples
    • Flight.Name: C20A flight location
    • Sample.Category: Ground sampling or atmosphere sampling
    • Collection.Date: Date of sampling
    • Protocol.REF: Sample concentration for all
    • is.neg: Whether the sample represents a negative control
  • seqtab_nochim.csv: tabulated sequences with chimeras removed
  • tax_table.csv: ASVs labeled with taxa annotated by silva132 database.
  • plots: subfolder containing plots generated from DADA2 pipeline.
    • fnFsquality.tiff: Quality score values of forward reads
    • fnRsquality.tiff: Quality score values of reverse reads
    • errorF.tiff: error rates, observed and predicted, for forward reads
    • errorR.tiff: error rates, observed and predicted, for reverse reads