UCSC Genome Browser Table Browser Tutorial

Step 1: Select Your Assembly

Use the Clade, Genome, and Assembly menus to choose your reference genome.

• Clade: Major organism group (e.g., Mammal, Vertebrate)
• Genome: Species (e.g., Human, Mouse)
• Assembly: Specific genome version (e.g., hg38)

Step 2: Select a Track

Choose the data track you want to work with. The Table Browser will pre-select your most recent track, but you can change it.

• Tracks are grouped similarly to those on the Genome Browser main page.
• Use "All Tracks" for comprehensive options.

Step 3: Select the Table

Each track may have one or more associated tables that store the data. Use the Table menu to select the relevant one.

Click the Data format description to explore:

• Table layout
• Related tables
• Joinable fields

Use "All Tables" to list all tables for the assembly.

Step 4: Define a Genomic Region

You can limit the output to a specific region or get data genome-wide. Whole-genome output may be unavailable for some tracks due to the large amount of data.

Options include:

• Entering a position (e.g., chr7:117199645-117356025)
• Typing a gene name and clicking Lookup
• Using Define regions to upload/paste multiple coordinates

Step 5: Select Output Format

Use the Output format dropdown to choose what type of file or fields you want returned.

Options include:

• All fields from the table
• Selected fields only
• File formats like BED, GTF, or custom tracks

Step 6: Submit Your Query

Click Get output to execute your query and view/download results. You can download results by entering a filename in the output filename field before clicking Get output.

You can also click Summary/statistics to preview:

• Record count
• Base coverage
• Item size ranges
• Time to compute