This is the code to process the RNA-seq data from "Enzyme-enhanced RNA isolation from biofilm producing bacteria." Usage functions for each file are as follows.

• processing_paired_reads.slurm is used on the UVA RIVANNA HPC and is the main code to trim, QC, align, and generate counts from the raw reads files.
• run_pipeline.sh is the shell script submitted to the UVA HPC to parallelize the processing of the raw reads.
• SMLT_differential_expression.Rmd is the code used to produce all the figures from the processed counts data.
• PA14_modified.gtf and Pseudomonas_aeruginosa_UCBPP-PA14_109.fna are the files used to generate the genome files for the STAR alignment.