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