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RAPTOR Tutorials

Welcome to the RAPTOR tutorial series! These hands-on guides will help you learn RAPTOR from basics to advanced usage.

📚 Tutorial Overview

Tutorial 1: Getting Started with RAPTOR

File: tutorial_01_getting_started.md
Level: Beginner
Time: 30 minutes
Prerequisites: RAPTOR installed

What you'll learn:

  • Basic RAPTOR commands
  • Data profiling workflow
  • How to interpret recommendations
  • Using simulated data

Start here if: You're new to RAPTOR or want a quick introduction.

Tutorial 2: Running Full Pipeline Benchmarking

File: tutorial_02_benchmarking.md
Level: Intermediate
Time: 3-6 hours (mostly automated)
Prerequisites: Tutorial 1 completed, all tools installed

What you'll learn:

  • Comprehensive pipeline comparison
  • Interpreting benchmark results
  • Making evidence-based decisions
  • Documentation for publications

Start here if: You need rigorous validation or are publishing results.

Tutorial 3: Working with Your Own RNA-seq Data

File: tutorial_03_real_data.md
Level: Intermediate
Time: 1-2 hours
Prerequisites: Tutorial 1 completed, your own data

What you'll learn:

  • Data preparation and formatting
  • Handling common data issues
  • Customizing analysis
  • Integration with existing workflows

Start here if: You have your own RNA-seq data ready to analyze.

🎯 Learning Paths

Path 1: Quick Start (1 hour)

For users who want to get started immediately:

  1. Tutorial 1 → Learn basics with simulated data
  2. Jump to your analysis!

Path 2: Comprehensive Learning (4-6 hours)

For users who want deep understanding:

  1. Tutorial 1 → Learn basics
  2. Tutorial 2 → Understand benchmarking
  3. Tutorial 3 → Apply to real data

Path 3: Real Data Focus (2-3 hours)

For users with data ready:

  1. Tutorial 1 (skim) → Understand concepts
  2. Tutorial 3 (detailed) → Apply to your data
  3. Tutorial 2 (if needed) → Validate choices

💡 Tutorial Features

Each tutorial includes:

  • ✅ Clear learning objectives
  • ✅ Step-by-step instructions
  • ✅ Expected outputs with examples
  • ✅ Troubleshooting for common issues
  • ✅ Best practices and tips
  • ✅ Real-world examples

🔧 Before You Start

System Requirements

Minimum for tutorials:

  • 8 GB RAM (16 GB recommended)
  • 20 GB free disk space
  • 4 CPU cores

For Tutorial 2 (benchmarking):

  • 32 GB RAM (64 GB recommended)
  • 100 GB free disk space
  • 8+ CPU cores

Software Requirements

Required:

  • Python 3.8+
  • RAPTOR v2.0.0+

For full pipeline runs:

  • All bioinformatics tools (see INSTALLATION.md)
  • R with Bioconductor packages

Installation

If you haven't installed RAPTOR yet:

# Quick install
pip install raptor-rnaseq

# With conda (includes all tools)
conda env create -f https://raw.githubusercontent.com/AyehBlk/RAPTOR/main/environment.yml
conda activate raptor

See INSTALLATION.md for detailed instructions.

📖 Additional Resources

Documentation

Community Support

🚀 Quick Reference

Common Commands

# Generate test data
raptor simulate --output test_data/ --size small

# Profile data
raptor profile --counts counts.csv --metadata metadata.csv

# Quick benchmark (3 pipelines)
raptor compare --data data/ --pipelines 3 4 6 --mode quick

# Full benchmark (all 8 pipelines)
raptor compare --data data/ --pipelines all --mode full

# Generate report
raptor report --results results/ --output report.html

# Get help
raptor --help
raptor profile --help

File Formats

Count Matrix (counts.csv):

gene_id,Sample1,Sample2,Sample3
Gene1,100,150,120
Gene2,50,45,60

Metadata (metadata.csv):

sample,condition,replicate
Sample1,Control,1
Sample2,Control,2
Sample3,Treatment,1

📜 Citation

If you use these tutorials in your research or teaching:

@software{raptor_tutorials2025,
  author = {Ayeh Bolouki},
  title = {RAPTOR Tutorials: Hands-on Guides for RNA-seq Pipeline Selection},
  year = {2025},
  publisher = {GitHub},
  url = {https://github.com/AyehBlk/RAPTOR/tree/main/docs/tutorials}
}

🎉 Ready to Start?

Jump into Tutorial 1: Getting Started now!

Tutorials created by Ayeh Bolouki
University of Namur, Belgium
For RAPTOR v2.0.0
MIT License

Last updated: January 2025