1) Copied data and checked md5's
- copydata.sh
- md5.sh

2) Make a file containing variables
-make_variables.sh

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

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

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

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

7) Run R script for creating count matrix and all downstream analysis
- NB_RNAseq_analysis_GLFit_CAMERA.Rmd

8) Index BAM files, move to one directory and run RSeQC geneBody_coverage.py
get_bam_files.sh
rseqc.sh