# Panprimate Browser Hub - Quick Start Guide

## Hub Location
```
/private/groups/cgl/pnhebbar/CAT2_smk/panprimate_output/browser_hub
```

## Hub Statistics
- **Total Size**: 7.3 GB
- **bigBed files**: 50 (5 tracks × 10 genomes)
- **Genome assemblies**: 10 (2bit format)
- **Track types**: 5 per genome

## Quick Access

### Option 1: Load to UCSC Genome Browser

1. Upload the `browser_hub` directory to a web server
2. Go to: https://genome.ucsc.edu/cgi-bin/hgHubConnect
3. Click "My Hubs" tab
4. Enter URL to `hub.txt`
5. Click "Add Hub"

### Option 2: Test Locally

```bash
cd /private/groups/cgl/pnhebbar/CAT2_smk/panprimate_output/browser_hub
python3 -m http.server 8000
# Then use: http://localhost:8000/hub.txt
```

## What's Included

### For Each Species:
1. **Consensus Genes** - Final annotation set (main track)
2. **TransMap** - Homology-based mappings
3. **Augustus TM** - Ab initio with transMap hints
4. **Augustus PB** - Ab initio with PacBio hints
5. **Liftoff** - Reference-based liftover

### Species List:
- Eulemur fulvus (PPG00246)
- Eulemur macaco (PPG00128)
- Eulemur rubriventer (PPG00129)
- Leontopithecus rosalia (PPG00786)
- Lagothrix lagotricha (PPG00525)
- Pithecia pithecia (PPG00239)
- Colobus angolensis (PPG00099)
- Mandrillus leucophaeus (PPG00232)
- Papio anubis (PPG00036)
- Macaca nemestrina (PPG00030)

## Files You Need to Share

To share this hub, you only need to upload the `browser_hub` directory to a web-accessible location. The key files are:

- `hub.txt` - Main hub configuration (point your browser here)
- `genomes.txt` - Defines all genomes
- `panprimate_description.html` - Hub description
- `[GENOME]/trackDb.txt` - Track definitions for each genome
- `[GENOME]/*.bb` - BigBed annotation files (50 total)
- `[GENOME]/*.2bit` - Genome sequences (10 total)

## Track Colors

- **Consensus Genes**: Blue (most important - shown by default)
- **TransMap**: Brown
- **Augustus TM**: Green
- **Augustus PB**: Purple
- **Liftoff**: Yellow-green

## Format Details

- **File format**: bigBed (bigGenePred)
- **Fields**: bed12+8 (includes gene names, CDS status, exon frames)
- **Searchable**: Yes (by transcript/gene name)
- **Compressed**: Yes (binary indexed format)

## Troubleshooting

### Hub won't load?
- Check that all files are web-accessible
- Verify `hub.txt` URL is correct
- Check file permissions (should be readable)

### Tracks not showing?
- Check `trackDb.txt` syntax
- Verify bigBed files exist and aren't empty
- Check chromosome names match between .2bit and .bb files

### Need help?
- See full documentation: `README.md`
- Contact: pnhebbar@ucsc.edu

## Regenerating

If you need to regenerate the hub:

```bash
cd /private/groups/cgl/pnhebbar/CAT2_smk
./run_create_hub.sh
```

---

**Hub Version**: 1.0  
**Created**: November 10, 2025  
**Format**: UCSC Track Hub with bigBed tracks