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SQANTI-browser Documentation

Welcome to SQANTI-browser! This tool converts SQANTI3 outputs into interactive UCSC Genome Browser track hubs.

Paniagua A, Blanco-Gómez C, Colomer Fernández A, Diekhans M, Conesa A, Monzó C. SQANTI-browser: visualization and curation of SQANTI3-classified long-read transcriptomes within the UCSC Genome Browser. bioRxiv (2026). DOI: 10.64898/2026.05.25.727625
Link to preprint

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🚀 New User? Start Here!

Never used SQANTI-browser before? Follow this path:

1. Quick Reference ⭐ - ONE-PAGE cheat sheet (start here!)
2. Installation Guide - Set up tools (5 minutes)
3. Usage Examples - Run your first conversion
4. Hosting Guide - Upload and view in UCSC

Done! Your tracks are now in UCSC. 🎉

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✨ Features

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

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📚 Complete Documentation Index

Quick Start:

• 🚀 Quick Reference - One-page cheat sheet ⭐
• ❓ FAQ - Frequently asked questions
• 📖 Glossary - Terms and definitions

Setup:

• Installation Guide
• Hosting Guide

Using SQANTI-browser:

• Usage Examples
• Command Line Reference
• Output Files

Features:

• Interactive HTML Tables
• Filtering in UCSC
• Trix Search Syntax
• Isoform Ordering

Advanced:

• Creating subset sessions
• Sharing sessions with collaborators
• Working with non-reference Genomes
• SQANTI-reads Integration
• Defining Custom Colors

AI Skills

• Installing and using SQANTI-browser's Claude Skill

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❓ Got Questions?

• FAQ - Answers to common questions
• Glossary - What do all these terms mean?
• Troubleshooting - Something not working?

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🔗 External Resources

• SQANTI3 Documentation - SQANTI3 reference
• UCSC Track Hub Documentation - UCSC reference
• GitHub Issues - Report bugs or request features

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💡 Pro Tips

1. Always start with the Quick Reference - It has everything you need on one page!
2. Use --tables to generate interactive HTML reports
3. Add --refGTF to compare with reference annotation
4. Run hubCheck before uploading to catch errors early
5. Check the FAQ before opening an issue

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Ready to get started? → Quick Reference