1) Make a file containing variables
-make_variables.sh

2) Quality control with FASTQC and MULTIQC
- fastqc.sh
- multiqc.sh 

3) Run STAR alignment 
- run_alignment.sh (uses STAR_align_and_count.sh)

4) Assess the aligment
- run_alignment_summary (uses assess_alignment.sh)

5) Get count information from STAR output ready to create count matrix in R
count_all_samples.sh

6) Run R script for creating count matrix and all downstream analysis
- acquired_resistance_analysis.Rmd