0. Environment Setup and Data Preparation

0. Environment Setup and Data Preparation

This section documents the initia directory structure establishment and creation of sym links pointing to the reference genome and raw Illumina datasets.

Workspace and coding

Create the root project directory structure. You can copy and paste the code provided in this repository, but make sure to update it with your own information.

# Navigate to the user home directory
cd /lustre/isaac24/proj/UTK0505/agonza84/EPP622-2026-SNPCalling

# Create a clean project directory. To keep your projects organized, I recommend matching your local folder name with your GitHub repository name. This makes it easier to link and track your work.
mkdir EPP622-2026-SNPCalling

# Change directory into the newly created folder
cd EPP622-2026-SNPCalling

# Clone the remote GitHub repository locally into the current directory
git clone https://github.com .

# Create the internal subdirectory layout
mkdir -p data/raw data/reference results

Dataset linkage

To preserve cluster storage resources and maintain absolute data integrity, symbolic links are generated to source the raw sequencing reads and the unmodified Saccharomyces cerevisiae reference genome directly from the shared project directories without duplicating files.

# Link the reference genome FASTA file 
ln -s /lustre/isaac24/proj/UTK0505/test2/ref/sacCer3.fa data/reference/s_cerevisiae_ref.fasta

# Link the 4 sets of simulated paired-end Illumina reads (Samples A, B, C, and D)
ln -s /lustre/isaac24/proj/UTK0505/test2/reads/Sample_A_R1.fastq.gz data/raw/Sample_A_R1.fastq.gz
ln -s /lustre/isaac24/proj/UTK0505/test2/reads/Sample_A_R2.fastq.gz data/raw/Sample_A_R2.fastq.gz

ln -s /lustre/isaac24/proj/UTK0505/test2/reads/Sample_B_R1.fastq.gz data/raw/Sample_B_R1.fastq.gz
ln -s /lustre/isaac24/proj/UTK0505/test2/reads/Sample_B_R2.fastq.gz data/raw/Sample_B_R2.fastq.gz

ln -s /lustre/isaac24/proj/UTK0505/test2/reads/Sample_C_R1.fastq.gz data/raw/Sample_C_R1.fastq.gz
ln -s /lustre/isaac24/proj/UTK0505/test2/reads/Sample_C_R2.fastq.gz data/raw/Sample_C_R2.fastq.gz

ln -s /lustre/isaac24/proj/UTK0505/test2/reads/Sample_D_R1.fastq.gz data/raw/Sample_D_R1.fastq.gz
ln -s /lustre/isaac24/proj/UTK0505/test2/reads/Sample_D_R2.fastq.gz data/raw/Sample_D_R2.fastq.gz

# Link the validation verification script and truth set for scoring variant calls
ln -s /lustre/isaac24/proj/UTK0505/test2/check/evaluate_snps_v4.py results/evaluate_snps_v4.py
ln -s /lustre/isaac24/proj/UTK0505/test2/check/truth_snps.vcf results/truth_snps.vcf

To verify your directory structure, run the command tree -L 3. This will display up to three levels deep from your current directory. If any symlinks are highlighted in red or blinking text, it means a link is broken. If this happens, go back and check your file paths.