-You can configure the tracks display font size, tooltip text size, label area width, and more by clicking the 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 font size, tooltip text size, label area width, and more by clicking the 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 d" (View - DNA), then select "extended case/color options" and adjust whether you want annotated bases colored, underlined, or bold, and click "submit".
+You can right-click most items to zoom in on them, or highlight them in the image. For gene tracks, you can also zoom to specific exons or codons.
+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, that can retrieve the internal organization of track data stanzas (trackDb), which is otherwise unavailable.
-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.
+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.
-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 interpretation, CNV interpretation, and non-coding SNV interpretation.
-The Track Collection Builder (My Data > Track Collection Builder) allows multiple signal tracks to be copied and grouped together into one composite. Signal tracks in a composite container 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 > Track Search) or the button underneath the tracks image. You can also search Public Hub data by using the Advanced tab.
-We offer 10Gb of free storage space to every user. First, log in or create an account, then go to Hub Upload under My Data > 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 track data in view can be found in the Download menu.
+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, 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 container. 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 constant indefinitely, making them suitable for publications as well. You can even customize the backend: 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. 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 > 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 daily!
-Want to use the Browser as a teaching tool? We offer teaching modules covering various genomic topics aimed at an undergraduate level. 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 > In Other Genomes) and selecting the QuickLift tracks box.
-While the Table Browser allows you to extract data from one source, 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.
+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, useful when analyzing exon sequencing data, which 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.
Have you ever wondered what we mean by "track" or what the difference is between "haplotype" and "fix" sequences? Take a look at the Genome Browser Glossary page for an explanation of these terms and many more.
+You can jump straight to an exon from the position box. Type TP53 exon 5 or NM_000546.6 exon 5 to land on that exon, or use the compact form BRCA2:e.10+2 to land a set number of bases into the flanking intron, which is handy for inspecting splice sites. See our searching help page for every kind of query we accept.
+Want the same data shown two ways at once? Click Duplicate track next to the display mode on most tracks' settings pages. The copy is its own track with independent filters, colors, and display mode, so a gene track can appear filtered and unfiltered at once.
+Lost track of what you have turned on? The Visible Tracks group sits at the top of the track list below the image and gathers every track you currently have visible into one place, so you can reconfigure or hide them without hunting through the track groups.
+Many track containers have a settings page that manages everything inside at once. You can show or hide the whole container while preserving each track's own settings, or use Apply to all visible tracks or Apply to all tracks to set display modes in bulk.
+You do not have to live with a track's default color. Right-click most annotation and signal tracks, choose Change Track Color, and pick from the palette. The new color applies to that track alone and stays with your session. Clear Enable color override to undo.
+Zoom in far enough and the Browser translates every coding exon into amino acids. Hovering over a residue reports its three letter and full name along with the c. and p. positions. The Base Position settings page also has a Complement the bases checkbox for reading the minus strand.
+You can display your own data in the Browser in seconds with Custom Tracks (My Data then Custom Tracks). Paste in a few lines of BED, VCF, GFF, or WIG, upload a file, or point us at a URL. No account is needed, though logging in lets you keep your data in a saved session.
+We offer interactive tutorials that walk you through the Browser step by step, on the site itself. From the tracks display, open Help then Interactive Tutorials for a guided tour of the tracks display, the Gateway, the Table Browser, Custom Tracks, or a clinical genetics workflow.
+You can send the region you are looking at straight to outside tools using View then In External Tools, or by typing "s" then "t". It hands your current sequence or coordinates to CRISPOR, CHOPCHOP, Primer3Plus, Primer-BLAST, NEBCutter, RNAfold, Pfam, Ensembl, and others, with no copying and pasting.
+Our In-Silico PCR tool (Tools then In-Silico PCR) takes a pair of primer sequences and returns the products they would amplify, along with the amplicon sequence and a link into the Browser. Set Target to a gene transcript set instead of the genome to handle RT-PCR primers that straddle intron boundaries.
+When you BLAT a sequence and are not sure which organism it came from, check Search all genomes to align it against all of our default assemblies at once. It is a quick way to identify an unknown sequence or spot contamination. There is also an I'm feeling lucky button that takes you directly to the best hit.
+The Table Browser does much more than dump out a table. You can paste a list of gene names or IDs to restrict the output to just those items, intersect or subtract one track against another, pull only exons or upstream regions rather than whole genes, and save a list of up to 1,000 regions to reuse across queries.
+Most track description pages have a Data Access section that tells you exactly how to get that track in bulk, whether through the Table Browser, the REST API, or a direct file on our downloads server. The same page also documents the methods, credits, and references behind the data.
+You can jump straight to the next annotation in a track instead of dragging around looking for it. Turn on Next/previous item navigation on the Configure page and gray arrows appear beside the track label. The white arrows on genes running off the edge of the image are on by default and step through exons one at a time.
+The button below the tracks image, or the shortcut "r" then "v", reverse complements the entire display and not just the DNA sequence. Every annotation flips to the minus strand, which makes a gene transcribed right to left far easier to read.
+Beyond our 230 or so natively hosted assemblies, our GenArk collection offers more than 50,000 NCBI assemblies, each already built with gene annotation and, for most eukaryotes, repeat annotation and alignments. We also curate more than 100 public track hubs that you can attach with one click from My Data then Track Hubs.
+Clicking a gene gives you far more than coordinates. The gene details page offers mRNA and protein sequence, genomic sequence with configurable flanking bases, RNA-Seq expression, protein domains and 3-D structures, orthologs in other species, GO annotations, pathways, disease links from MalaCards and GeneReviews, and a graph of published gene interactions.
+Has your display gotten cluttered? The button below the tracks image, or the shortcut "h" then "a", clears every track at once. For a completely fresh start, Genome Browser then Reset All User Settings restores the original defaults. Note that a reset also removes your custom tracks and attached hubs, so save a session first if you want to keep them.
+Have a question about the Browser or the data in it? Our public mailing list is answered by the people who build and curate the Browser, and the archive is publicly searchable, so you can often find your answer before asking. There is also a private list for questions involving confidential data, and a low volume announcements list for new releases.
+Our Poster Gallery collects more than 30 conference posters we have presented since 2015, each a one page tour of a set of features. Topics include variant interpretation, track hub storage, quickLift, pangenome data, and transposable elements, and every one is free to download.
+Not sure what sequences an assembly actually contains? View then Chromosomes, or the shortcut "v" then "s", lists every chromosome and scaffold with its size, and offers the assembly's chrom.sizes and alias name files to download. This is especially handy on newer or less familiar assemblies, where the sequence names may not be what you expect.
+Assemblies often carry several names for the same sequence. Hover the information icon beside the position to see the alternatives, such as 17, CM000679.2, and NC_000017.11 for human chr17. Any of these names will work in the position box and in your own custom tracks, hubs, and bigBed or bigWig files, so there is no need to convert first.