SQANTI-browser

SQANTI-browser is a tool that converts SQANTI3 transcriptome analysis outputs into UCSC Genome Browser track hubs for interactive visualization.

⚠️WARNING: SQANTI-browser is currently under beta testing.

Features

• 🎨 Color-coded transcripts by structural category
• 🔍 Advanced filtering with dropdowns and range sliders
• 📊 Per-category tracks for easy exploration
• 🔎 Trix search for finding isoforms using keywords for any attribute
• 📋 Interactive HTML tables with export capabilities

Documentation

📖 See the Wiki for detailed documentation:

• Installation Guide
• Usage Examples
• Filtering in UCSC
• Trix Search Syntax
• Isoform Ordering
• Command Line Reference
• Output File Formats
• Troubleshooting

Quick Start

1. Install Dependencies

# Install UCSC tools
bash install_ucsc_tools.sh

# Install Python dependencies
pip install -r requirements.txt

2. Run the Converter

python sqanti3_to_UCSC.py \
    --gtf your_corrected.gtf \
    --classification your_classification.txt \
    --output my_hub \
    --genome hg38

3. Upload to UCSC

1. Upload the output directory to a web server (e.g., GitHub)
2. Go to UCSC Genome Browser → My Data → Track Hubs → Connected Hubs
3. Enter the URL to your publicly available hub.txt file into the URL window
4. Click Add Hub

Common Options

Option	Description
--tables	Generate interactive HTML tables for each category
--github-repo user/repo	Auto-generate GitHub raw URLs
--sort-by iso_exp	Sort isoforms by expression (or length, FL, etc.)
--no-category-tracks	Only generate the main track
--star-sj SJ.out.tab	Include STAR splice junctions track

Color Legend

Category	Color	Hex Code
Full-splice match (FSM)	Blue	#6BAED6
Incomplete-splice match (ISM)	Orange	#FC8D59
Novel in catalog (NIC)	Green	#78C679
Novel not in catalog (NNC)	Red	#EE6A50
Genic	Gray	#969696
Antisense	Teal	#66C2A4
Fusion	Gold	#DAA520
Intergenic	Salmon	#E9967A
Genic intron	Cyan	#41B6C4

License

GNU General Public License v3.0 - see LICENSE

Citation

If you use this tool, please cite:

• https://github.com/conesalab/SQANTI-browser
• Pardo-Palacios, F.J., Arzalluz-Luque, A. et al. SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02229-2
• Perez, G. et al. The UCSC Genome Browser database: 2025 update. Nucleic Acids Res (2025). https://doi.org/10.1093/nar/gkae974