Does any one have good pipeline for analyzing bacterial RNA seq data using R? I found many pipelines and tutorials using eukaryotic data, but it is very tough for bacterial sequencing data.
You can check on https://cs.wellesley.edu/~btjaden/Rockhopper/ for Bacterial RNA analysis. Pipeline in R you can use rSeqTU package https://rdrr.io/github/s18692001/rSeqTU/