UCSC Genome Browser Table Browser Tutorial
The UCSC Table Browser is a flexible tool for accessing and exporting data from genome browser tracks. This tutorial introduces the Table Browser interface and demonstrates how to:
- Select a genome and assembly
- Choose a track and table
- Define a region of interest or use identifiers
- Customize output formats
- Download or view extracted results
Learning materials
Table Browser Overview
A screenshot highlighting the layout and key elements of the Table Browser interface.
Guided Walkthrough
Step-by-step guidance for using the Table Browser to extract data for your analysis.
Interactive Tutorial
An in-browser walkthrough that introduces the Table Browser interface and workflow.
Table Browser Overview
Guided Walkthrough
Step 1: Select Your Assembly
Use the Genome search box to choose your reference genome. Start typing a species name, common name, or assembly ID and pick a match from the list that drops down. The Table Browser reloads on that assembly, and Assembly shows which one you are using.
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 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
- Using to upload/paste multiple coordinates
- Pasting or uploading a list of identifiers, such as gene names or accessions, with or to return only those items
Optional: filter, subset, or combine tracks
The Filter and Intersection tools, in the Subset, combine, compare with another track section, let you narrow down or combine data before you get output.
Click next to Filter to keep only the rows that match conditions you set, for example genes on the plus strand or items above a score cutoff. A filter stays in place until you clear it, so you can switch tracks or regions and rerun the same query.
Click next to Intersection to combine the current track with a second one. This answers questions like which SNPs fall inside RefSeq coding exons, or which of your regions overlap a peak track. You pick the second track and whether to keep the rows that overlap or the ones that don't.
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 selected table returns the table as it is stored.
- Selected fields from primary and related tables lets you pick just the columns you want, and pull in columns from related tables in the same query. This is the easiest way to get something like gene names next to coordinates without downloading the whole table.
- File formats like BED, GTF, or a custom track you can load back into the browser.
- Sequence returns the DNA, or protein for some tracks, covered by your table.
Step 6: Submit Your Query
Click to execute your query and view/download results. You can download results by entering a filename in the output filename field before clicking .
You can also click to preview:
- Record count
- Base coverage
- Item size ranges
- Time to compute