espA Mathematical Modeling

Introduction

This repository contains the codes of Jiazheng Miao's (MBI Class of 2025) Capstone Project, a mathematical modeling on the expression level of espA in Mycobacterium tuberculosis.

Pipeline

Execute the scripts according to the following order:

1. sbatch_download.sh: Download data listed in dna_accession.txt and rna_accession.txt
2. sbatch_dnaseq_pe.sh: Process paired-ended DNA-seq data
3. sbatch_dnaseq_se.sh: Process single-ended DNA-seq data
4. sbatch_rnaseq.sh: Process RNA-seq data
5. organize_data.py: Aggregate VCF files to a CSV file, convert RNA read counts to LogFKPM, and screen for RD8/RD236a deletions
6. merge_replicates.R: Combine identified variants and average the expression level across the technique replicates
7. pca.R: Decompose the variant matrix (espA regulatory region excluded) into PCs
8. modeling.Rmd: Perform the modeling