--- a/COBRAxy/docs/quickstart.md	Mon Oct 27 12:33:08 2025 +0000
+++ b/COBRAxy/docs/quickstart.md	Tue Oct 28 10:44:07 2025 +0000
@@ -38,7 +38,6 @@
 
 ```bash
 # Generate RAS scores using built-in ENGRO2 model
-# Note: -td is optional and auto-detected after pip install
 ras_generator \
   -in sample_expression.tsv \
   -ra ras_scores.tsv \
@@ -62,7 +61,6 @@
 
 ```bash
 # Create pathway maps with statistical analysis
-# Note: -td is optional and auto-detected after pip install
 marea \
   -using_RAS true \
   -input_data ras_scores.tsv \
@@ -97,19 +95,19 @@
 
 ### Learn More About the Analysis
 
-- **[Understanding RAS](/tools/ras-generator.md)** - How activity scores are computed
-- **[MAREA Analysis](/tools/marea.md)** - Statistical enrichment methods  
+- **[Understanding RAS](tools/ras-generator)** - How activity scores are computed
+- **[MAREA Analysis](tools/marea)** - Statistical enrichment methods  
 - **[Data Flow](getting-started.md#analysis-workflows)** - Complete workflow overview
 
 ### Try Advanced Features
 
 - **[Flux Sampling](tutorials/workflow.md#flux-simulation-workflow)** - Predict metabolic flux distributions
-- **[Galaxy Interface](/tutorials/galaxy-setup.md)** - Web-based analysis
+- **[Galaxy Interface](tutorials/galaxy-setup)** - Web-based analysis
 
 ### Use Your Own Data
 
-- **[Data Formats](/tutorials/data-formats.md)** - Prepare your expression data
-- **[Troubleshooting](/troubleshooting.md)** - Common issues and solutions
+- **[Data Formats](tutorials/data-formats)** - Prepare your expression data
+- **[Troubleshooting](troubleshooting)** - Common issues and solutions
 
 ## Complete Example Pipeline
 
@@ -125,7 +123,6 @@
 EOF
 
 # Run analysis pipeline
-# Note: -td is optional and auto-detected after pip install
 ras_generator -in expression.tsv -ra ras.tsv -rs ENGRO2
 marea -using_RAS true -input_data ras.tsv -choice_map ENGRO2 -gs true -idop maps
 
@@ -140,4 +137,4 @@
 1. **Check Prerequisites**: Ensure COBRAxy is properly installed
 2. **Verify File Format**: Make sure your data is tab-separated TSV
 3. **Review Logs**: Look for error messages in the terminal output
-4. **Consult Guides**: [Troubleshooting](/troubleshooting.md) and [Installation](/installation.md)
\ No newline at end of file
+4. **Consult Guides**: [Troubleshooting](troubleshooting) and [Installation](installation)
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