This repository contains code applied to total RNA shotgun paired sequences, from trimming to binning into rRNA and mRNA (in bash), as well as rRNA based community analysis using phyloseq and vegan (in R). Total RNA was extracted from eroding permafrost, the raw data can be found here:
All copyright is due to: McMurdie, P. J., and Holmes, S. (2013). phyloseq : An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS One 8. doi:10.1371/journal.pone.0061217. Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., et al. (2020). vegan: Community Ecology Package. R package version 2.5-7. Available at: https://cran.r-project.org/package=vegan%0A.