Genome Mapping Analysis

This repository contains scripts for analyzing genome mapping data from SAM files. The scripts extract mapping information, summarize mapped reads across genes, and identify multi-mapped reads.

Structure

• Scripts/: Contains the Python scripts for data processing and analysis.
• data/: Directory to store input SAM files.
• results/: Directory to store output CSV files.

Scripts

1. Multi-Mapper Analysis

The multi_mapper_analysis.py script identifies and counts multi-mapped and unique-mapped reads in SAM files.

2. Unmapped Analysis

The unmapped_analysis_script.py script merges data from multiple SAM files, summarizes mapped reads per gene, and filters genes using read-count thresholds.

Usage

1. Install the required packages:

   pip install -r requirements.txt

2. Run the multi-mapper analysis script:

   python Scripts/multi_mapper_analysis.py

3. Run the unmapped analysis script:

   python Scripts/unmapped_analysis_script.py

Requirements

• pandas
• pysam

Example Data

Place your SAM files in the data/ directory.