Audience: First-time users and students learning genomics Time: 15-20 minutes Prerequisites: A modern web browser (Chrome, Firefox, Safari, Edge) Last updated: Session 23 (2026-01-22)
- Understanding the gBeta interface
- Navigating the genome (search, pan, zoom)
- Loading local and remote data files
- Using basic filters and highlights
- Customizing themes and colors
Open gBeta in your web browser. You'll see a clean interface with:
- Header (top): Search bar and navigation controls
- Sidebar (left): Track list and file loading
- Main area (center): Genomic visualization canvas
- GQL Console tab (bottom): Click to open the advanced query interface
The browser starts with a default view of chromosome 1 in the human genome.
Note
Gene tracks load automatically for most assemblies. You don't need to find gene annotations yourself.
gBeta gives you three ways in: the Search Bar for quick tasks, the GQL Console for advanced work, and the Ask AI panel for asking questions in plain English.
The search bar in the header is perfect for quick navigation:
- Type a gene name:
TP53 - Type coordinates:
chr17:7668421-7687490 - Type simple commands:
zoom in,pan left 10kb
The search bar uses basic pattern matching - it works offline and responds instantly. Results appear inline next to the search bar.
Tip
Press / on your keyboard to quickly focus the search bar.
For more complex queries, use the GQL Console:
- Click the GQL Console tab at the bottom of the screen (or press
Cmd+`` /Ctrl+``) - The console panel slides up, showing:
- Natural Language input (top-left): Type questions in plain English
- GQL input (bottom-left): View and edit the generated query
- Results panel (center): Clickable list of results
- History/Saved (right): Session history and saved queries
When to use the Console:
- Complex queries:
SELECT GENES INTERSECT variants ORDER BY length DESC - AI-powered natural language: "show me genes with high-impact variants" (requires AI setup)
- Saving queries for reproducibility
- Sharing queries via URL
- Exporting query collections
Key difference: The Search Bar is quick and local. The GQL Console is powerful and can use AI for natural language understanding.
Click the floating 💬 Ask AI button (bottom-right) and chat in plain English: "which genes here have variants?", "show pathogenic variants in TP53", "what's the fewest variants in any gene?" It runs the query for you and shows the results as a ranked, clickable list — click a row to jump there — and asks a follow-up question when your request is ambiguous. Requires AI setup; everything deterministic (coordinates, gene lookup, hand-written GQL) works without it.
For this tutorial, we'll use the Search Bar. You can try the Console and Ask AI later — see Tutorial 5: Reproducible Analysis for advanced usage.
Let's find TP53, a famous tumor suppressor gene often mutated in cancer.
- Click the search bar at the top (or press
/on your keyboard) - Type:
TP53 - Press Enter
gBeta navigates to chromosome 17 where TP53 is located. You should see the coordinate display change to something like chr17:7,668,421-7,687,490.
When you typed TP53, gBeta:
- Recognized it as a gene name
- Looked up its coordinates (chr17:7668421-7687490)
- Navigated the view to show that region
- Click the + button to zoom in (see more detail)
- Click the - button to zoom out (see more context)
- Scroll up to zoom in
- Scroll down to zoom out
Tip
Scroll with your mouse wheel to zoom in and out quickly.
Type in the search bar:
zoom in
or
zoom out
Zoom in several times until you can see individual features (exons, CDS regions). Then zoom out to see the gene in its genomic context.
Move left or right along the chromosome.
Click and drag on the canvas to pan.
pan left 10kb
pan right 10kb
Pan around to explore the region near TP53. What other genes are nearby?
gBeta can display your own genomic data. Let's try loading a file.
Indexed formats (recommended for large files):
| Format | Extensions | Index | Use for |
|---|---|---|---|
| BigBed | .bb, .bigbed | Built-in | Intervals |
| BigWig | .bw, .bigwig | Built-in | Signal/coverage |
| BAM | .bam | .bam.bai | Alignments |
| CRAM | .cram | .cram.crai | Alignments (smaller) |
| Tabix VCF | .vcf.gz | .vcf.gz.tbi | Variants |
| Tabix GFF | .gff.gz | .gff.gz.tbi | Gene annotations |
| Tabix BED | .bed.gz | .bed.gz.tbi | Intervals |
These work both locally (drag and drop) and remotely (paste URL). gBeta only loads the data you're viewing, so even multi-gigabyte files open instantly.
Tip
For indexed files with external indexes (.bai, .tbi), select both files together when loading locally.
Plain text formats (small files only):
| Format | Extension | Use for |
|---|---|---|
| BED | .bed | Small interval lists |
| GFF3 | .gff3, .gff | Small annotations |
| VCF | .vcf | Small variant sets |
| bedGraph | .bedgraph | Small signal data |
These are loaded entirely into memory - fine for files under a few MB, but use indexed formats for larger data.
Option A: From URL (recommended for large files)
- Click the URL tab in the sidebar
- Paste a URL to any indexed format (BigBed, BigWig, BAM, tabix, etc.)
- Click + to add the track
- The index file is auto-discovered (must be at same URL path)
Option B: Local files
- Look at the Add Tracks section in the sidebar
- The File tab is selected by default
- Click Drop or browse to select files
- For indexed files (BAM, tabix), select both the data file AND index file together
Option C: Drag and drop
- Drag files from your computer onto the gBeta window
- For indexed files, drag both the data and index files together
- Drop anywhere on the canvas
Warning
Chromosome names must match between your files and the assembly (e.g., chr1 vs 1).
Your data appears as a new track below the main view. Each track shows a different type of information at the same genomic position.
When viewing gene annotations (GFF3 files), you can filter to focus on specific feature types.
filter type=exon
Exons (coding parts of genes) appear bright; everything else dims.
filter type=CDS
filter strand=+
Shows features on the plus (forward) strand.
clear filters
Returns to showing all features normally.
Mark regions of interest with highlights.
highlight chr17:7670000-7675000
A colored overlay appears over that region.
clear highlights
gBeta offers multiple themes and color palettes.
Click the Settings button (gear icon) in the header.
In the Display tab:
- Light (default) - Clean, print-ready
- Dark - Easier on eyes in low light
- High-Contrast - Maximum readability
Choose from colorblind-safe palettes:
- Set2 (default) - Soft, distinct colors
- Dark2 - Bolder colors
- Paired - High contrast pairs
Changes apply immediately and persist across sessions.
Load a remote BAM file to see alignments:
- Select assembly E. coli K-12 MG1655 from the assembly dropdown
- Click the URL tab in the sidebar
- Paste this URL:
https://pub-cdedc141a021461d9db8432b0ec926d7.r2.dev/test/ecoli-test.bam - Click + to add the track
- Navigate to
NC_000913.3:100000-100500 - Zoom in to see individual reads
You've just loaded remote alignment data without downloading anything!
| Action | How |
|---|---|
| Search for gene | Type gene name, press Enter |
| Go to coordinates | Type chr17:1000000-2000000 |
| Zoom in | Scroll up, or type zoom in |
| Zoom out | Scroll down, or type zoom out |
| Pan | Click and drag, or type pan left 10kb |
| Load file | Drag and drop |
| Load remote file | Sidebar URL tab, paste URL |
| Filter features | Type filter type=exon |
| Clear filters | Type clear filters |
| Highlight region | Type highlight chr17:1000-2000 |
| Change theme | Settings > Display |
Why can't I find my gene?
gBeta has a built-in index of common genes. If your gene isn't found:
- Check the spelling
- Try the official gene symbol (BRCA1, not "breast cancer gene")
- Load a GFF3 file containing your gene annotations
My file won't load!
Check that:
- The file has the correct extension (.bed, .gff3, .vcf, .bedgraph)
- The file isn't too large (stay under 100MB for best performance)
- The chromosome names match (chr1 vs 1)
Everything disappeared!
You might have zoomed out too far. Try:
- Searching for a gene to navigate back
- Type
navigate chr1:1-1000000for a default view
The tracks overlap!
Each track needs space. Try:
- Closing tracks you don't need
- Zooming out for a wider view
You now know how to:
- Navigate the gBeta interface
- Search for genes and navigate to coordinates
- Zoom in/out and pan around the genome
- Load local files via drag-and-drop or the File tab
- Load remote files via the URL tab
- Filter features by type or strand
- Highlight regions of interest
- Customize themes and color palettes
Now that you know the basics, explore these topics:
- Tutorial 2: Exploring Genes - Work with variant data
- GQL Examples - More commands to try
- GQL Manual - Complete command reference
Try this sequence on your own:
- Navigate to BRCA1:
search gene BRCA1 - Zoom in 3 times
- Filter to show only exons:
filter type=exon - Pan left to see more of the gene
- Clear the filter:
clear filters - Highlight a region of interest
Congratulations! You've learned the fundamentals of genome browsing.