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Welcome to SQANTI-browser! This tool converts SQANTI3 outputs into interactive UCSC Genome Browser track hubs.
Never used SQANTI-browser before? Follow this path:
- Quick Reference ⭐ - ONE-PAGE cheat sheet (start here!)
- Installation Guide - Set up tools (5 minutes)
- Usage Examples - Run your first conversion
- Hosting Guide - Upload and view in UCSC
Done! Your tracks are now in UCSC. 🎉
| Feature | Description |
|---|---|
| 🎨 Color-coded transcripts | Automatic coloring by structural category |
| 📋 Dropdown filters | Easy filtering with dropdown menus |
| 📊 Range definition | Definition of ranges for numeric filtering |
| 🔎 Trix search | Full-text search in UCSC browser |
| 📈 Interactive HTML tables | Sortable, filterable, exportable tables |
| 🗂️ Per-category tracks | Separate tracks for each category |
| 🧬 Validation tracks | STAR junctions, CAGE peaks, PolyA peaks |
| 🔬 Custom genomes | Support for .2bit files |
Quick Start:
- 🚀 Quick Reference - One-page cheat sheet ⭐
- ❓ FAQ - Frequently asked questions
- 📖 Glossary - Terms and definitions
Setup:
Using SQANTI-browser:
Features:
Advanced:
- FAQ - Answers to common questions
- Glossary - What do all these terms mean?
- Troubleshooting - Something not working?
- SQANTI3 Documentation - SQANTI3 reference
- UCSC Track Hub Documentation - UCSC reference
- GitHub Issues - Report bugs or request features
- Always start with the Quick Reference - It has everything you need on one page!
-
Use
--tablesto generate interactive HTML reports -
Add
--refGTFto compare with reference annotation -
Run
hubCheckbefore uploading to catch errors early - Check the FAQ before opening an issue
Ready to get started? → Quick Reference