This repository contains the RMarkdown script and associated data files to reproduce the analyses described in Bender et al., Quantification of variation and the impact of biomass in targeted 16S rRNA gene microbiome studies.
A decent number of packages are required - see the top of the R script for details. Installation is up to the user.
In addition to the raw FASTQ files available via SRA (BioProject: PRJNA415628), we also include more helpful intermediate files in the /data folder. These can be downloaded and used directly with the R script. Some details about the contents of each file:
- BLAST_results.parsed.txt - taxonomic classification by BLAST, useful for obtaining species-level labels for each ASV
- mapping.txt - mapping file with metadata variables
- merged_seqtab.nochim.rds - RDS object containing the amplicon sequence variant (ASV) table produced by DADA2
- metadata_types.txt - file containing some information about the metadata variables (outcomes) of interest
- qPCR.txt - qPCR data used in the biomass analysis
- taxa_coloring.txt - some pretty colors for genus-level barplots
Questions/comments can be submitted via the issue tracker or by email to fanli (at) mednet (dot) ucla (dot) edu.