modtector
Overview
Key Features
Quick Start
Installation
Example Dataset
Basic Usage
Workflow Overview
Version Information
Support
Project Links
Citation
Documentation Contents
Documentation Sections
Getting Started
User Documentation
Support & Development
Quick Navigation
Installation Guide
System Requirements
Minimum Requirements
Required Dependencies
Installing Rust
Linux/macOS
Windows
Installing modtector
Method 1: Build from Source (Recommended)
Method 2: Install via Cargo
Dependencies
Platform-Specific Notes
Linux
macOS
Windows
Verification
Troubleshooting
Common Issues
Getting Help
Next Steps
Uninstallation
Quick Start Guide
Prerequisites
Example Dataset
Step 1: Generate Pileup Data
Step 2: Calculate Reactivity Scores
Step 3: Normalize Reactivity Signals
Step 4: Duet Ensemble Analysis
Step 5: Generate Visualizations
Step 6: Evaluate Accuracy
Expected Outputs
Key Output Files
Understanding the Results
Reactivity Scores
Evaluation Metrics
Common Issues and Solutions
Issue 1: Low Coverage
Issue 2: Poor Normalization
Issue 3: Low Evaluation Scores
Next Steps
Getting Help
Tips for Success
User Guide
Table of Contents
Understanding RNA Modifications
What are RNA Modifications?
Common RNA Modifications
Detection Methods
modtector Workflow
Overview
Step-by-Step Process
Data Preparation
Input Requirements
BAM Files
Reference Sequences
Secondary Structure Files
Data Quality Checks
Batch Processing and Single-cell Mode
Batch Mode (
--batch
)
Single-cell Unified Mode (
--single-cell
)
Signal Types
Stop Signals
Characteristics
Analysis
Mutation Signals
Characteristics
Analysis
Combined Analysis
Normalization Methods
Purpose
Available Methods
1. Percentile28 Normalization
2. Winsor90 Normalization
3. Boxplot Normalization
Window-Based Normalization
Fixed Windows
Dynamic Windows
Sliding Windows
Reactivity Calculation
Purpose
Calculation Methods
Stop Signal Methods
Mutation Signal Methods
Parameters
Pseudocount
Maximum Score
Evaluation Metrics
Purpose
Available Metrics
1. Area Under the Curve (AUC)
2. F1-Score
3. Accuracy
4. Sensitivity (Recall)
5. Specificity
6. Positive Predictive Value (PPV)
7. Negative Predictive Value (NPV)
Evaluation Process
Output Files
Visualization
Purpose
Available Plots
1. Signal Distribution Plots
2. Reactivity Plots
3. ROC Curves
4. PR Curves
5. Comparison Plots
6. RNA Structure SVG Plots
7. Interactive HTML Visualizations
SVG Plotting
Overview
SVG-Only Mode
Multi-Signal SVG Plotting
Interactive HTML Visualization
Single Signal SVG Plotting
SVG Plotting with Alignment
SVG Output Files
Plotting Options
Basic Plotting
With Reactivity Data
Custom Thresholds
With Genome Annotation
Advanced Features
Multi-threading
Window Analysis
Fixed Windows
Dynamic Windows
Base-Specific Analysis
Statistical Testing
Auto-shift Correction
Base Matching
Best Practices
Data Quality
Parameter Selection
Performance Optimization
Result Interpretation
Troubleshooting
Documentation
Common Workflows
Basic Workflow
Advanced Workflow
Command Reference
Overview
count - Data Processing
Usage
Options
Examples
Batch and Single-cell Modes
Output Format
norm - Signal Normalization
Usage
Options
Normalization Methods
Examples
reactivity - Reactivity Calculation
Usage
Options
Reactivity Methods
Stop Signal Methods
Mutation Signal Methods
K-Factor Prediction Methods
Examples
compare - Sample Comparison
Usage
Options
Comparison Modes
Statistical Tests
Examples
evaluate - Accuracy Evaluation
Usage
Options
Examples
plot - Visualization
Usage
Regular Mode
SVG-Only Mode
Options
SVG Plotting Options
Examples
Regular Plotting
SVG-Only Mode
Combined Mode (Regular + SVG)
SVG Plotting Features
Signal Type Support
Strand Selection
Base Filtering
Alignment Support
Output Files
Regular Mode Output
SVG Mode Output
Combined Mode Output
duet - Dynamic Ensemble Decomposition
Usage
Options
Outputs
Progress Reporting
Examples
extract - Extract Gene Regions from Count Results
Usage
Options
How It Works
Gene Matching
Examples
Output Format
File Naming
Input Formats
CSV Format (default)
bam-readcount Format
Performance Optimization
Notes
convert - Format Conversion
Usage
Options
Supported Input Formats
Examples
Input Format (bamreadcount)
Output Format (modtector pileup)
Conversion Details
Performance
Progress Reporting
Error Handling
Use Cases
Notes
correct - PCR Bias Correction
Usage
Options
How It Works
Method Details
Examples
Output Format
Use Cases
Notes
Global Options
Output Files
Common Output Formats
File Naming Conventions
Best Practices
Troubleshooting
Common Issues
Getting Help
Examples and Tutorials
Table of Contents
Basic Example
Scenario
Data
Step-by-Step Process
1. Generate Pileup Data
2. Calculate Reactivity
3. Normalize Reactivity Signals
4. Generate Plots
5. Evaluate Accuracy
Expected Outputs
Advanced Example
Scenario
Data
Advanced Workflow
1. Batch Processing with Windowing
2. Advanced Normalization
3. Multiple Reactivity Methods
4. Statistical Comparison
5. Comprehensive Evaluation
SVG Plotting Examples
Scenario
Data Requirements
Basic SVG Plotting
1. Simple SVG Plot (SVG-Only Mode)
2. Multi-Signal SVG Plotting
3. Single Signal SVG Plotting
Advanced SVG Plotting
4. SVG Plotting with Alignment
5. Negative Strand SVG Plotting
6. Both Strands SVG Plotting
Combined Mode (Regular + SVG)
7. Generate Both Regular and SVG Plots
Real-World Examples
Example 1: Human 18S rRNA Structure
Example 2: E.coli 16S rRNA Structure
Example 3: DMS-seq Specific Analysis
SVG Output Files
File Naming Convention
SVG File Structure
Troubleshooting SVG Plotting
Common Issues
Quality Control
Best Practices
Batch Processing
Scenario
Batch Script Example
Parallel Processing
Custom Analysis
Scenario
Region-Specific Analysis
Custom Normalization Parameters
Custom Reactivity Parameters
Troubleshooting Examples
Low Coverage Issue
Memory Issues
Poor Normalization
Low Evaluation Scores
Performance Optimization
Large Dataset Processing
Memory Optimization
Disk Space Management
Real-World Examples
Example 1: m6A Detection
Example 2: m1A Detection
Example 3: Pseudouridine Detection
Quality Control Examples
Data Quality Assessment
Result Validation
Integration Examples
Snakemake Workflow
Nextflow Workflow
Troubleshooting Guide
Table of Contents
Installation Issues
Rust Not Found
Build Failures
Permission Errors
Data Processing Issues
BAM File Issues
Reference Sequence Issues
Low Coverage
Alignment Quality Issues
Performance Issues
Slow Processing
High CPU Usage
Disk I/O Issues
Output Quality Issues
Poor Normalization
Low Reactivity Scores
Poor Evaluation Scores
Memory and Resource Issues
Out of Memory
Disk Space Issues
File Format Issues
CSV Format Problems
Structure File Issues
BAM Index Issues
Getting Help
Log Files
Debug Mode
Common Error Messages
“BAM file not found”
“Reference sequence not found”
“Insufficient memory”
“Low coverage”
“Poor alignment quality”
Reporting Issues
Community Support
Professional Support
Prevention Tips
Best Practices
Regular Maintenance
Contributing to modtector
Table of Contents
Getting Started
Prerequisites
Fork and Clone
Development Setup
Contributing Guidelines
Types of Contributions
Contribution Process
Branch Naming
Code Style
Rust Style Guidelines
Code Formatting
Linting
Documentation
Testing
Test Structure
Running Tests
Test Data
Integration Tests
Documentation
Code Documentation
User Documentation
Documentation Standards
Submitting Changes
Pull Request Process
Pull Request Template
Review Process
Issue Reporting
Bug Reports
Feature Requests
Issue Template
Development Workflow
Daily Workflow
Release Process
Code of Conduct
Our Pledge
Expected Behavior
Unacceptable Behavior
Enforcement
Getting Help
Communication Channels
Mentorship
Resources
Recognition
modtector
Index
Index