|
492
|
1 # Quick Start Guide
|
|
|
2
|
|
|
3 Get started with COBRAxy! This guide walks you through your first metabolic analysis.
|
|
|
4
|
|
|
5 ## Step 1: Verify Installation
|
|
|
6
|
|
|
7 Test that COBRAxy is working:
|
|
|
8
|
|
|
9 ```bash
|
|
|
10 # Check if tools are available
|
|
|
11 ras_generator --help
|
|
|
12
|
|
|
13 # Should display help text without errors
|
|
|
14 ```
|
|
|
15
|
|
|
16 ## Step 2: Download Sample Data
|
|
|
17
|
|
|
18 Create a sample gene expression file:
|
|
|
19
|
|
|
20 ```bash
|
|
|
21 # Create sample data
|
|
|
22 cat > sample_expression.tsv << 'EOF'
|
|
|
23 Gene_ID Control_1 Control_2 Treatment_1 Treatment_2
|
|
|
24 HGNC:5 8.5 9.2 15.7 14.3
|
|
|
25 HGNC:10 3.2 4.1 8.8 7.9
|
|
|
26 HGNC:15 7.9 8.2 4.4 5.1
|
|
|
27 HGNC:25 12.1 13.5 18.2 17.8
|
|
|
28 HGNC:30 6.3 7.1 11.5 10.8
|
|
|
29 HGNC:55 14.2 15.8 22.1 21.3
|
|
|
30 HGNC:80 5.7 6.4 2.8 3.2
|
|
|
31 HGNC:100 9.8 10.5 16.7 15.9
|
|
|
32 EOF
|
|
|
33 ```
|
|
|
34
|
|
|
35 ## Step 3: Generate Activity Scores
|
|
|
36
|
|
|
37 Compute Reaction Activity Scores (RAS) from your gene expression:
|
|
|
38
|
|
|
39 ```bash
|
|
|
40 # Generate RAS scores using built-in ENGRO2 model
|
|
|
41 ras_generator -td $(pwd) \
|
|
|
42 -in sample_expression.tsv \
|
|
|
43 -ra ras_scores.tsv \
|
|
|
44 -rs ENGRO2
|
|
|
45
|
|
|
46 # Check output
|
|
|
47 head ras_scores.tsv
|
|
|
48 ```
|
|
|
49
|
|
|
50 **Expected output**:
|
|
|
51 ```tsv
|
|
|
52 Reactions Control_1 Control_2 Treatment_1 Treatment_2
|
|
|
53 R_HEX1 8.5 9.2 15.7 14.3
|
|
|
54 R_PGI 7.9 8.2 4.4 5.1
|
|
|
55 ...
|
|
|
56 ```
|
|
|
57
|
|
|
58 ## Step 4: Create Pathway Visualizations
|
|
|
59
|
|
|
60 Generate enriched pathway maps with statistical analysis:
|
|
|
61
|
|
|
62 ```bash
|
|
|
63 # Create pathway maps with statistical analysis
|
|
|
64 marea -td $(pwd) \
|
|
|
65 -using_RAS true \
|
|
|
66 -input_data ras_scores.tsv \
|
|
|
67 -choice_map ENGRO2 \
|
|
|
68 -gs true \
|
|
|
69 -idop pathway_maps
|
|
|
70
|
|
|
71 # Check results
|
|
|
72 ls pathway_maps/
|
|
|
73 ```
|
|
|
74
|
|
|
75 **Expected output**: SVG files with colored pathway maps showing metabolic changes.
|
|
|
76
|
|
|
77 ## Step 5: View Results
|
|
|
78
|
|
|
79 Open the generated pathway maps:
|
|
|
80
|
|
|
81 ```bash
|
|
|
82 # Open SVG files in your browser or image viewer
|
|
|
83 # Files will be in pathway_maps/ directory
|
|
|
84 firefox pathway_maps/*.svg # Linux
|
|
|
85 open pathway_maps/*.svg # macOS
|
|
|
86 ```
|
|
|
87
|
|
|
88 ## What Just Happened?
|
|
|
89
|
|
|
90 1. **RAS Generation**: Mapped gene expression to metabolic reactions using GPR rules
|
|
|
91 2. **Statistical Analysis**: Identified significantly altered pathways between conditions
|
|
|
92 3. **Visualization**: Created colored pathway maps highlighting metabolic changes
|
|
|
93
|
|
|
94 ## Next Steps
|
|
|
95
|
|
|
96 ### Learn More About the Analysis
|
|
|
97
|
|
|
98 - **[Understanding RAS](tools/ras-generator.md)** - How activity scores are computed
|
|
|
99 - **[MAREA Analysis](tools/marea.md)** - Statistical enrichment methods
|
|
|
100 - **[Data Flow](getting-started.md#analysis-workflows)** - Complete workflow overview
|
|
|
101
|
|
|
102 ### Try Advanced Features
|
|
|
103
|
|
|
104 - **[Flux Sampling](tutorials/workflow.md#flux-simulation-workflow)** - Predict metabolic flux distributions
|
|
|
105 - **[Python API](tutorials/python-api.md)** - Integrate into scripts and pipelines
|
|
|
106 - **[Galaxy Interface](tutorials/galaxy-setup.md)** - Web-based analysis
|
|
|
107
|
|
|
108 ### Use Your Own Data
|
|
|
109
|
|
|
110 - **[Data Formats](tutorials/data-formats.md)** - Prepare your expression data
|
|
|
111 - **[Troubleshooting](troubleshooting.md)** - Common issues and solutions
|
|
|
112
|
|
|
113 ## Complete Example Pipeline
|
|
|
114
|
|
|
115 Here's the full command sequence for reference:
|
|
|
116
|
|
|
117 ```bash
|
|
|
118 # Set up
|
|
|
119 cd /path/to/analysis/
|
|
|
120
|
|
|
121 # Generate sample data (or use your own)
|
|
|
122 cat > expression.tsv << 'EOF'
|
|
|
123 [your gene expression data]
|
|
|
124 EOF
|
|
|
125
|
|
|
126 # Run analysis pipeline
|
|
|
127 ras_generator -td /path/to/COBRAxy -in expression.tsv -ra ras.tsv -rs ENGRO2
|
|
|
128 marea -td /path/to/COBRAxy -using_RAS true -input_data ras.tsv -choice_map ENGRO2 -gs true -idop maps
|
|
|
129
|
|
|
130 # View results
|
|
|
131 ls maps/*.svg
|
|
|
132 ```
|
|
|
133
|
|
|
134 ## Getting Help
|
|
|
135
|
|
|
136 If something doesn't work:
|
|
|
137
|
|
|
138 1. **Check Prerequisites**: Ensure COBRAxy is properly installed
|
|
|
139 2. **Verify File Format**: Make sure your data is tab-separated TSV
|
|
|
140 3. **Review Logs**: Look for error messages in the terminal output
|
|
|
141 4. **Consult Guides**: [Troubleshooting](troubleshooting.md) and [Installation](installation.md)
|
|
|
142
|
|
|
143 **Still stuck?** Ask for help in [GitHub Discussions](https://github.com/CompBtBs/COBRAxy/discussions).
|
|
|
144
|
|
|
145 ## Summary
|
|
|
146
|
|
|
147 🎉 **Congratulations!** You've completed your first COBRAxy analysis. You now know how to:
|
|
|
148
|
|
|
149 - ✅ Generate metabolic activity scores from gene expression
|
|
|
150 - ✅ Create statistical pathway visualizations
|
|
|
151 - ✅ Interpret basic COBRAxy outputs
|
|
|
152
|
|
|
153 Ready for more? Explore the [full documentation](/) to unlock COBRAxy's complete potential! |
