DMD vs WT Single-End RNA-seq Analysis Pipeline

Nextflow DSL2 assignment page

• Repository: github.com/berfinida/pipeline
• Dataset: GSE156496 / SRP278118
• Samples: WT1, WT2, DMD1, DMD2
• Report PDF: Open report

This project implements FastQC, fastp, Salmon, MultiQC, and TPM-based descriptive comparison.

Descriptive TPM Outputs

• dmd_vs_wt_summary.tsv
• top10_upregulated.tsv
• top10_downregulated.tsv

How To Run

export JAVA_HOME=/Library/Java/JavaVirtualMachines/temurin-17.jdk/Contents/Home
export PATH="$JAVA_HOME/bin:$HOME/miniforge3/bin:$PATH"

nextflow run main.nf \
  -profile conda \
  --samplesheet samplesheet.csv \
  --outdir results \
  --salmon_index "$PWD/refs/salmon_index" \
  -resume

MultiQC

MultiQC findings are summarized in the assignment report PDF. Raw MultiQC artifacts are excluded from GitHub due to size policy.