Autocore is a bioinformatics pipeline for processing and analyzing RNA-seq data, with a focus on autoimmune diseases. The repository contains scripts and resources for data prefetching, alignment, quantification, and downstream analysis.

• IBD (Inflammatory Bowel Disease): Chronic inflammation of the digestive tract, including Crohn's Disease(CD) and Ulcerative Colitis(UC) which can ultimatley lead to Colorectal Cancer (CRC).
• Psoriasis: Autoimmune skin disorder causing red, scaly patches.
• RA (Rheumatoid Arthritis): Autoimmune disorder affecting joints, causing pain and swelling.
• Sjörgen's Syndrome: Autoimmune disease targeting moisture-producing glands, leading to dry mouth and eyes.
• SLE (Systemic Lupus Erythematosus): Multi-system autoimmune disease affecting skin, joints, kidneys, and other organs.

Each disease module contains:

• Disease-specific metadata
• Count files
• Analysis scripts
• Plots and tables

1. Clone the repository:

   git clone https://github.com/sarachitgaran/Autocore.git
   cd Autocore

2. Install dependencies:

   • R
   • HISAT2, SAMtools, HTSeq

3. Run the pipeline:

   • Execute the shell scripts in order (0_prefetch.sh → 4_htseq_count.sh).
   • Use R scripts in disease folders for downstream analysis.

All Linux-based processing scripts are located in the Bash_Scripts directory, with each step of the pipeline implemented as a separate SLURM batch file. The resulting gene count files are collected in the Count_Files directory. Differential gene expression (DGE) analysis and its results—including plots and tables—are organized in the Differential_Gene_Expression_Analysis directory. Further downstream analyses are stored in the Downstream_Analysis drectory.

Contributions are welcome! Please open issues or submit pull requests for improvements or bug fixes.