What is Dr. Zubair Khalid's research focus?

Dr. Zubair Khalid specializes in molecular virology, mRNA vaccine development, and computational biology, with a focus on avian pathogens like IBDV and Avian Reovirus.

Where is Dr. Zubair Khalid currently working?

Dr. Zubair Khalid is a Postdoctoral Research Associate at the University of Maryland (UMD), specifically within the Department of Animal and Avian Sciences.

UCSC Genome Browser: Beginner Tutorial and Tips

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-09-20

The UCSC Genome Browser is a free, web-based tool for viewing a genome and the annotations placed on top of it. By the end of this tutorial you will be able to pick the correct assembly, jump to a gene or a coordinate, turn annotation tracks on and off, search a DNA sequence with BLAT, and export a clean table of features for downstream work. You need only three things: a modern web browser, an internet connection, and a clear idea of which genome assembly your data uses. No installation is required, and nothing in this walkthrough depends on a local server or a cloud account. The browser has served the research community since 2001 and now covers thousands of assemblies across many organisms [1][2].

What the UCSC Genome Browser Actually Is

The Browser is a graphical viewer. It places annotation tracks beneath genome coordinate positions so you can correlate different kinds of information in one window [3]. The annotations come from two places: tracks computed and maintained by the UCSC Genome Bioinformatics group, and tracks submitted by scientists worldwide [3]. You can also upload your own experimental results or annotation sets as a custom track, which means your BED, wiggle, BAM, or VCF data can sit alongside the public tracks [3][4].

The underlying data are stored in database tables. Those tables can be viewed, downloaded, and manipulated through a second web application, the UCSC Table Browser [5]. This pairing matters. The graphic page answers "what does this region look like," and the Table Browser answers "give me every row that matches this query." Most beginners live in the graphic page and then discover the Table Browser when they need a file.

A third concept is the track data hub. A hub is a remotely hosted, internet-accessible collection of genome annotations that is organized, configured, and fully integrated into the Browser through the familiar interface [6]. Hubs let an individual or a consortium publish a dataset without maintaining a mirror of the whole Browser [6]. The Genome Archive, or GenArk, system builds on this idea and provides browsers for thousands of NCBI assemblies, each with gene models, repeat masks, BLAT, and in silico PCR [7].

Step 1: Choose the Correct Genome Assembly

This is the single most consequential decision in the whole workflow. Coordinates are meaningless without an assembly. The same gene sits at different base positions on hg19 and hg38, so a coordinate copied from a paper that used hg19 will point somewhere else if you are viewing hg38. Assembly choice changes coordinates, full stop.

hg38 versus hg19

Human data in the Browser is most often placed on either hg19 (also called GRCh37) or hg38 (also called GRCh38). Newer publications and most current reference resources use hg38. Older datasets, some legacy variant files, and a large body of clinical literature use hg19. Neither is "wrong." The mistake is mixing them.

A practical rule: read the methods section of the paper, the header of the variant file, or the README of the dataset before you type a coordinate. If the source says GRCh37 or hg19, load hg19. If it says GRCh38 or hg38, load hg38. If it says nothing, stop and find out.

How to switch assemblies

On the Browser gateway page, the assembly is selected from a dropdown before you enter the Browser. You can also change it from inside the Browser by using the "Genome" menu at the top of the graphic page and picking a different assembly. When you switch, the Browser keeps your position in the genome but recalculates what is under the cursor for the new coordinate system, so always re-check the locus.

Converting coordinates with liftOver

When you must move a coordinate from one assembly to another, use liftOver. liftOver takes a file of intervals in one assembly and maps them to the equivalent intervals in another, using the chain files that describe the alignment between the two assemblies. Some intervals map cleanly, some map to more than one place, and some do not map at all because the sequence was rearranged, duplicated, or removed. Those unmapped intervals are the ones to inspect by hand. Never assume a coordinate is portable just because a tool produced an output line.

Step 2: Search a Gene or a Coordinate

The search box at the top of the gateway page accepts several input types. You can type a gene symbol, a genomic coordinate range, a single base position, an rsID for a variant, or a keyword.

Searching by gene symbol

Type the symbol, for example BRCA1, and press submit. The Browser returns a list of matching items across the tracks that are currently in the database. Click the correct gene model to jump to its locus. If the symbol is ambiguous, the results page will show several candidates with their chromosome and position so you can pick.

Searching by coordinate

The coordinate format is chr:start-end using 1-based coordinates. For example:

chr17:43,044,295-43,125,364

This is the BRCA1 region on hg38. Note the commas in the numbers and the colon between chromosome and range. The Browser accepts ranges with or without commas, but commas make long coordinates readable.

Searching by rsID

Type a dbSNP identifier such as rs80357906 and the Browser jumps to that variant's position and highlights it in the variation tracks. This is the fastest way to check what a variant looks like in context.

Navigating once you are there

The graphic page has a row of navigation controls above the tracks. The zoom buttons change the scale by a fixed factor. The "base position" track shows the ruler at the top, and you can drag the ruler left or right to pan. The drag-and-zoom feature lets you click and drag a region to zoom into it directly [8]. At the far right of the ruler, the "zoom in" and "zoom out" links give finer control. The size of the displayed region is shown in the top bar, so you always know how many bases you are looking at.

Step 3: Add and Configure Tracks

Tracks are grouped by type. The main groups you will use as a beginner are gene and gene prediction tracks, comparative genomics tracks (including conservation), variation and repeats, expression, regulation, and phenotype. The Recommended Track Sets feature on hg38 gives you a curated starting point so you are not confronted with hundreds of checkboxes at once [9].

Turning tracks on and off

Scroll to the bottom of the graphic page and click "configure tracks" or use the track group links under the image. Each track has a dropdown that sets its display mode. The common modes are:

hide: the track is not drawn.
dense: the track is drawn as a compact summary with no labels.
squish: items are drawn at reduced height with some labels.
pack: each item gets its own row, compact.
full: each item gets its own row with full labels and details.

Start with "pack" for gene tracks and "dense" for conservation. Switch to "full" only when you need to read individual feature names.

Reading a gene track

A gene track shows exons as thick blocks and introns as thin lines with arrowheads that indicate the direction of transcription. A vertical line marks the transcription start. Click any item to open a details page with the gene name, the transcript, the strand, and links to external resources. The 2025 update added a popup dialog that shows item details without navigating away from the main page, and gene prediction tracks now support right-click options for zooming and precise navigation [1].

Reading a conservation track

Conservation tracks display a score at each position, computed from a multiple alignment of many species. Higher scores mean the position is more conserved across the alignment. Use conservation as a hypothesis generator, not as proof of function. A conserved base is more likely to matter, but conservation alone does not tell you what a base does.

Reading a variation track

Variation tracks show known variants, their alleles, and often their frequency in reference populations. The gnomAD track on hg38 is a common choice for population allele frequency [1]. Variation tracks can be dense, so use the display mode controls and the "next item" navigation to step through features one at a time.

Custom tracks and hubs

If you have your own data, you can add it as a custom track by pasting a URL or uploading a file in a supported format. Custom tracks are stored with your session and can be backed up [10]. For larger, reusable datasets, a track hub is the better option because the data stay on your server and the Browser reads them from there [6]. The chromAlias system means you no longer have to rename your sequence names to the UCSC standard before displaying custom annotations [9]. Tools like MakeHub automate the generation of assembly hubs for novel genomes, which is useful when your organism does not yet have a public browser [11].

Step 4: Use BLAT for Sequence Searches

BLAT is the Browser's alignment tool. It takes a DNA or protein sequence and finds where it matches the genome. Use it when you have a sequence but not a coordinate: a primer pair, a cloned fragment, a transcript, or a protein.

When to use BLAT instead of the position search

Use the position search when you already know the gene or the coordinate. Use BLAT when you have sequence and need to find its location. BLAT is also the right tool for checking whether a primer pair is unique in the genome, which is a common quality control step before running a PCR-based assay.

Running a BLAT search

From the top menu, choose "Tools" and then "BLAT." Paste your sequence into the text box, or upload a file. Select the genome and assembly, choose the sequence type (DNA or protein), and submit. The BLAT results page lists matches ranked by score, with the chromosome, the coordinates, the strand, and the percent identity. Click a match to open it in the Browser.

The web BLAT tool can search against all genomes, which is useful when you are not sure which assembly your sequence came from [10]. Public hub assemblies now also support BLAT and in silico PCR capabilities [12].

Interpreting BLAT output

A single high-identity match means your sequence is unique. Multiple matches with similar scores mean the sequence is repeated or has a close paralog. Partial matches at the ends usually mean your sequence extends beyond the aligned region, which is common with primers that sit near an assembly gap. Always look at the alignment itself, not just the score.

Step 5: Export Data with the Table Browser

The Table Browser is where you turn a visual region into a file. It is a full-featured graphical interface that allows querying, filtering, and intersection of data tables [4]. Open it from the "Tools" menu or the top navigation bar.

The basic export workflow

Set the clade, genome, and assembly. These must match the data you want.
Set the group and track. For example, group "Genes and Gene Predictions," track "GENCODE" or "UCSC Genes."
Set the table. Each track may have several underlying tables.
Set the region. Choose "genome" for the whole assembly, or paste a coordinate range for a specific locus.
Set the output format. BED is the most portable for intervals. Other options include tab-separated values and FASTA for sequence.
Optionally add a filter, such as a minimum conservation score or a specific variant class.
Click "get output" to preview, then "send output to file" to download.

A worked example

Suppose you want every exon of every protein-coding gene on chromosome 17 in hg38, as a BED file. Set genome to Human, assembly to hg38, group to Genes and Gene Predictions, track to the current gene set, table to the exon table, region to chr17, and output format to BED. The preview shows the first rows. Send to file and you have a BED file you can load into any interval tool.

Intersecting two tracks

The Table Browser can intersect two tables, which is how you answer questions like "which variants fall inside conserved regions" or "which peaks overlap a promoter." Set the first track and region, then use the "intersection" option to pick the second track. Choose whether to keep the first table's rows, the second table's rows, or both. The output contains only the rows that satisfy the overlap rule.

Checking your export

Before you trust a file, check three things. First, the chromosome names should match the assembly you intend to use downstream (chr1 versus 1 is a common mismatch). Second, the number of rows should be plausible for the region you selected. Third, spot-check two or three coordinates by pasting them back into the Browser and confirming the feature is there.

Sharing Your Work with Sessions

A saved session stores your assembly, your position, your track configuration, and your custom tracks. The Saved Session feature allows users to store and share customized views, which is useful for organizing multiple lines of inquiry [4]. To share, save the session, then send the session URL to a collaborator. They open the same view you see. This is the cleanest way to hand off a figure or a locus to a colleague, because it removes any ambiguity about which tracks were on.

Sessions also protect you from losing work. If you spend twenty minutes configuring tracks, save before you navigate away.

Common Tasks and Their Menu Paths

Task	Menu path
Change assembly	Genome menu, then select assembly
Jump to a gene	Gateway search box, type symbol
Jump to a coordinate	Gateway search box, type `chr:start-end`
Jump to a variant	Gateway search box, type rsID
Add or hide tracks	Bottom of graphic page, configure tracks
Change track display mode	Track dropdown, choose hide dense squish pack full
Align a sequence	Tools menu, BLAT
Export a table	Tools menu, Table Browser
Convert coordinates	Tools menu, liftOver
Save or share a view	My Data menu, My Sessions
Add a custom track	My Data menu, Custom Tracks
Add a track hub	My Data menu, Track Hubs

A Decision Path for a New Locus

The workflow below shows the order of decisions from a question to an exported file.

flowchart TD
    A[Start with a question] --> B{Do you have a coordinate}
    B -->|No| C[Search gene or rsID]
    B -->|No sequence| D[Run BLAT]
    C --> E[Confirm assembly]
    D --> E
    E --> F[Load tracks]
    F --> G[Inspect locus]
    G --> H{Need a file}
    H -->|Yes| I[Open Table Browser]
    H -->|No| J[Save session]
    I --> K[Set filters]
    K --> L[Download output]

Common Mistakes and Limitations

The most frequent error is using the wrong assembly. A coordinate from an hg19 paper viewed on hg38 will land in the wrong place, and the gene track may still show a plausible-looking gene nearby, which makes the error hard to notice. Always confirm the assembly before you interpret anything.

The second most frequent error is assuming that a track's presence means the feature is real and functional. Tracks are annotations. Some are experimentally validated, some are computational predictions, and some are aggregations of heterogeneous sources. Read the track description before you cite it.

A third error is treating the Browser as an analysis package. It is a visualization tool. It does not run a regression, it does not compute a p-value, and it does not correct for multiple testing. If you need statistics, export the data and analyze it in the appropriate software.

A fourth error is ignoring the resolution limits of a track. Some tracks are only meaningful at certain zoom levels. A conservation score at a single base is noisy. A gene model at a chromosome-wide view is a smear. Zoom to the scale the track was designed for.

A fifth error is forgetting that custom track data are your responsibility. The Browser will display what you upload, including errors. Validate your file format and your coordinates before uploading.

Finally, remember that the Browser is one view of the data. It is not a substitute for reading the primary literature, checking the assembly documentation, or consulting a domain expert when a result is surprising. Individual research questions need appropriate statistical and biological expertise.

Tips That Save Time

Use the Recommended Track Sets on hg38 as a starting configuration, then add tracks as needed [9]. This avoids the paralysis of hundreds of checkboxes.

Use the multi-region display configuration to view several loci side by side, which is helpful when comparing paralogs or isoforms [13].

Use the right-click options on gene prediction tracks to zoom and navigate precisely instead of dragging [1].

Use the popup dialog to read item details without losing your place on the page [1].

Use track hubs instead of custom tracks when your dataset is large or when you want to share it with others without re-uploading [6].

Use the session backup feature before you make large changes to a complex configuration [10].

Use the Genome Archive search on the gateway page when your organism is not one of the common model species [7].

Frequently Asked Questions

What is the UCSC Genome Browser used for?

It is used to view a genome and its annotations in one window. You can inspect genes, conservation, variation, and regulatory data at any scale from a single base to a whole chromosome [4].

How do I know whether to use hg38 or hg19?

Use the assembly named by your data source. If a paper or file says GRCh37 or hg19, use hg19. If it says GRCh38 or hg38, use hg38. Never mix them without converting coordinates.

How do I convert coordinates between assemblies?

Use liftOver from the Tools menu. It maps intervals from one assembly to another using chain files. Check the unmapped intervals manually because some regions do not convert cleanly.

What is BLAT and when should I use it?

BLAT is the Browser's sequence alignment tool. Use it when you have a DNA or protein sequence and need to find where it matches the genome, such as when checking primer specificity.

How do I download data from the UCSC Genome Browser?

Open the Table Browser from the Tools menu, set the genome, assembly, track, table, and region, choose an output format, and send the output to a file [5].

Can I share my UCSC Genome Browser view with a collaborator?

Yes. Save the view as a session and send the session URL. Your collaborator will see the same assembly, position, and track configuration [4].

What is a track hub?

A track hub is a remotely hosted collection of annotations that is integrated into the Browser through the normal interface. It lets you publish datasets without running a mirror [6].

Does the UCSC Genome Browser do statistical analysis?

No. It is a visualization tool. Export your data and run statistical tests in the appropriate software.