Built under Bash version 4.3.48 and R version 3.5.1

Unix Packages: SRA Toolkit version 2.9.0, BBTools v38, STAR v2.6.9c, RSEM v1.3.1, GNU parallel 2017 (optional)
R Packages: tximport, EdgeR, limma, ggplot, ggpubr, reshape2

Minimum: 16GB RAM
Recommended: 32GB+ RAM

1. FASTA: Genome Assembly of your choice as a single FASTA file.
   
2. GTF: Gene Annotation File in GTF format
3. TX2GENE: A Transcript ID to Gene ID Conversion table for RSEM. IMPORTANT: Has to match IDs in your GTF file.

1. Create a Tab-delimited file with SRA Accession IDs in first column
   
2. Specify your inputs in Config.sh File
   
3. Navigate to the RNA-Seq-Pipeline directory
4. Run the following command:
   

./Run.sh