About the Project
This project presents a production-style bioinformatics workflow for RNA-seq analysis using public DMD vs WT mouse data. The pipeline is implemented in Nextflow DSL2 and designed for reproducibility, maintainability, and transparent computational reporting.
It processes single-end RNA-seq reads from raw FASTQ through quality control, trimming, transcript quantification, and final expression matrix generation for downstream comparative analysis.
Workflow Steps
FASTQ
FastQC
fastp
Salmon
MultiQC
Expression Matrix
Dataset Information
GEO: GSE156496
SRA: SRP278118
Biological context: WT vs DMD DeltaEx51 mouse tibialis anterior muscle RNA-seq
Results
Expression matrix generation for all samples
TPM-based comparison between WT and DMD groups
Top upregulated and downregulated transcript extraction
Fully reproducible end-to-end workflow execution
Technologies Used
Nextflow DSL2
Python
pandas
Salmon
FastQC
fastp
MultiQC
Conda
GitHub
Project Metrics
4RNA-seq samples
Publicreal FASTQ dataset
Automatedpipeline orchestration
End-to-endreproducibility