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