You can configure the tracks display text size, tooltip text size, label area width, and more by clicking the button below the image, using the keyboard shortcut (type "c" then "f"), or via the menu (Genome Browser then Configure).
You can configure the tracks display text size, tooltip text size, label area width, and more by clicking the button below the image, using the keyboard shortcut (type "c" then "f"), or via the menu (Genome Browser then Configure).
You can color and download DNA sequence based on any data tracks. While on the track display, type "v" then "d" (View then DNA Sequence), then select "Extended case/color options" and adjust whether you want annotated bases colored, underlined, or bold, and click "submit".
From the Base Position track description page you can enter motifs to highlight, edit the amino acid reading frames display, and even add a title to the Browser image.
We offer a REST API available under the menu (Downloads then REST API) that can return almost all data available in the Browser in JSON format. It also has additional endpoints, such as /list/schema, which reports every field in a track along with its type and description, and /list/tracks, which returns the configuration settings that drive a track's display.
We offer a scalable (vector-based) graphic of your current tracks display, suitable for use in publications, via the menu (View then PDF). This PDF can then be used with your editor of choice (e.g. Adobe Illustrator) to edit and export the image as PNG, TIFF, SVG, or PDF with the dpi (dots per inch value) of your choice.
-You can download the PNG image of your current display via right click -> View image, or by changing hgTracks in the URL bar to hgRenderTracks. The hgRenderTracks approach provides programmatic access to the PNG image. For publications, use the menu option (View then PDF) for a scalable image.
+You can download the PNG image of your current display via right click -> View image, or by changing hgTracks in the URL bar to hgRenderTracks. The hgRenderTracks approach provides programmatic access to the PNG image. For a scalable image, add hgt.psOutput=on to the hgRenderTracks URL to get a PDF, or use the menu option (View then PDF).
We offer Recommended Track Sets for hg19 and hg38 that display a pre-set browser configuration based on specific areas of interest. These include SNV and CNV interpretation, non-coding variants, exon relevance, problematic regions, and expert panel sets for BRCA1/BRCA2 and Lynch syndrome.
The Track Collection Builder (My Data then Track Collection Builder) allows multiple signal tracks to be copied and grouped together into one collection. Signal tracks in a collection can then be overlaid, auto-scaled, sorted by similarity, and more.
The best way to find what data is available for an assembly is Track Search, found by keyboard shortcut (t then s), in the menu bar (Genome Browser then Track Search) or the button underneath the tracks image. You can also search Public Hub data by using the Advanced tab.
We offer 10 GB of free storage space with every account. First, log in or create an account, then go to Hub Upload under My Data then Track Hubs. You can also upload bigBed and bigWig files for immediate visualization.
You can download all visible data in the current browser region from the tracks display. This allows for improved reproducibility, writing variant reports, or publications. Download Current Track Data can be found in the Downloads menu.
We support various kinds of searching from the tracks display address bar. You can use HGVS terms (NM_198056.2:c.1A>C), gnomAD style variants (1-55051215-G-GA), BLAT sequences directly from the search box, documentation, and more.
We have a page that provides information about accessibility options in the UCSC Genome Browser, including internal configuration settings and third-party tools.
The best way to find an assembly is the search box on our Gateway page. If your assembly of interest is not available, you can request nearly any Genbank assembly as long as it has a GCA or GCF accession.
The best way to share the URL of a Genome Browser display is with a Session link. Displays from copying and pasting the URL from the address bar can change over time, but session links remain stable, which makes them suitable for publications as well. You can even give one a short, readable name: https://genome.ucsc.edu/s/view/HappyNewYear
You can slice the Browser display into different regions, stitched together into a single display, using Multi-region mode. A common use of this mode is to display only the exons of a gene, which is useful when analyzing exon sequencing data. That exon-only view has its own shortcut ("e" then "v"). Enable this mode with the button next to the tracks display search bar.
Our Short Match tool allows you to search for any short (2-30 base) sequence. All matches of the motif within the displayed position range are then shown. You can find it by clicking into the Short Match track in the Mapping and Sequencing track group, or via the menu bar from the tracks display (Genome Browser then Short Exact DNA Match).
Be sure to check our home page often! We regularly update our news with the latest releases, our Meetings and Workshops (come say hello!), and the Sharing data section which displays images and descriptions from our Public Sessions created by users like you. Also, new tips like this one every weekday!
Want to use the Browser as a teaching tool? We offer teaching material covering various genomic topics, written for students and educators alike. We also have various slide decks, contact us for more details!
You can convert annotations between different assemblies using the LiftOver tool. You can also use the QuickLift feature to immediately lift all your visible annotations from the tracks display using the menu (View then In Other Genomes (Convert)) and selecting the QuickLift tracks box. See our QuickLift help page for details.
While the Table Browser allows you to extract data from one track at a time, the Data Integrator allows you to select track items that overlap by position, and output all (or selected) fields from up to 5 tracks at a time.