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Carolina Monzó edited this page Dec 15, 2025
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Welcome to the SQANTI-browser documentation! This tool converts SQANTI3 transcriptome analysis outputs into UCSC Genome Browser track hubs.
- 📦 Installation Guide
- 🚀 Usage Examples
- 🔍 Filtering in UCSC
- 🔎 Trix Search Syntax
- 📊 Isoform Ordering
- 💻 Command Line Reference
- 📁 Output File Formats
- 🔧 Troubleshooting
| Feature | Description |
|---|---|
| 🎨 Color-coded transcripts | Automatic coloring by structural category |
| 📋 Dropdown filters | Easy filtering with dropdown menus |
| 📊 Range sliders | Numeric filtering with sliders |
| 🔎 Trix search | Full-text search in UCSC browser |
| 📈 Interactive HTML tables | Sortable, filterable, exportable tables |
| 🗂️ Per-category tracks | Separate tracks for each category |
- Install the required tools: Installation Guide
- Run the converter: Usage Examples
- Upload to UCSC and explore your data!
| Category | Color | Hex Code | Description |
|---|---|---|---|
| Full-splice match | Blue | #6BAED6 | Perfect match to reference |
| Incomplete-splice match | Orange | #FC8D59 | Partial match to reference |
| Novel in catalog | Green | #78C679 | Novel combination of known junctions |
| Novel not in catalog | Red | #EE6A50 | Contains novel junctions |
| Genic | Gray | #969696 | Overlaps gene but no splice match |
| Antisense | Teal | #66C2A4 | Antisense to annotated gene |
| Fusion | Gold | #DAA520 | Spans multiple genes |
| Intergenic | Salmon | #E9967A | Between annotated genes |
| Genic intron | Cyan | #41B6C4 | Within intron of annotated gene |
- GitHub Issues - Report bugs or request features
- SQANTI3 Documentation - SQANTI3 reference
- UCSC Track Hub Documentation - UCSC reference