3b9272e66fdac648a90baf02dc5eb696a286fdf1 mspeir Sat Mar 28 16:06:45 2026 -0700 revamping page, refs #36894 diff --git docs/index.md docs/index.md index e04395941d6..d7144ff96e1 100644 --- docs/index.md +++ docs/index.md @@ -1,13 +1,127 @@ --- title: "Genome Browser Documentation" --- Browse all UCSC Genome Browser documentation by topic. -## Tutorials +New to the Genome Browser? Start with our [Genome Browser Basics +tutorial](/docs/tutorials/gb101.html), a 15-minute walkthrough of the +interface, navigation, and track display. You can also browse our +[glossary](/docs/genomeBrowserGlossary.html) to learn common terms used throughout +this documentation. -[Tutorials](tutorials/index.html) +## Using the Genome Browser Interface and Tools -## Hubs +The Genome Browser offers a dynamic interface for visualizing genomic data on +a variety of genome assemblies. In addition to visualization, there are several tools +for extracting data from the current visualization. -[Hubs Basics](hubs/hubBasics.html) +### Tutorials +We offer detailed step-by-step tutorials for several of our tools: + +| Title | Description | Link | +| - | - | - | +| Genome Browser Basics | Covers basics of the UCSC Genome Browser track interface | [View Tutorial](/docs/tutorials/gb101.html) | +| Gateway Page | Learn to find genome assemblies | [View Tutorial](/docs/tutorials/gatewayTutorial.html) | +| Table Browser | Introduces Table Browser queries | [View Tutorial](/docs/tutorials/tableBrowserTutorial.html) | +| Custom Tracks | Upload your custom annotations | [View Tutorial](/docs/tutorials/customTrackTutorial.html) | + +Navigate to our [Tutorial index](/docs/tutorials/index.html) to see them all. + +### Video tutorials +Our [training page](/training/index.html) has short how-to videos covering common +tasks like saving sessions, using BLAT and isPCR, finding SNPs in a gene, and +using Multi-Region View. We also offer in-person and virtual workshops, +[contact us](/docs/contacts.html) to host one at your institution. + +## Understanding Genome Browser Assemblies and Annotations + +The Genome Browser allows for the visualization of various annotations on +a wide variety of genome assemblies. A genome assembly is a reconstruction of +an organism's complete DNA sequence from shorter sequenced fragments. Different +assemblies of the same species may exist as sequencing technology improves +(e.g., hg19 vs. hg38 for human). + +- Use our [gateway page](/cgi-bin/hgGateway) to access popular assemblies or + search for an assembly of interest. Learn more from our + [tutorial](/docs/tutorials/gatewayTutorial.html). +- If your assembly is not available, [request it](/assemblySearch.html). + +The Genome Browser displays annotations as horizontal "tracks" layered beneath +the genome coordinate ruler. These tracks fall into several major categories: + +- Genes and Gene Predictions: curated and predicted gene models (GENCODE, + RefSeq, Augustus) +- Regulation: transcription factor binding, histone marks, DNase + hypersensitivity (ENCODE, Roadmap Epigenomics) +- Comparative Genomics: cross-species conservation scores, alignments (PhyloP, + PhastCons, chain/net) +- Variation: SNPs, structural variants, clinical variants (dbSNP, ClinVar, + gnomAD) +- Repeats: repetitive elements (RepeatMasker, Simple Repeats) +- Mapping and Sequencing: assembly structure, gaps, chromosome bands + +Each track has its own description page (accessible by clicking the track name) +with details on the data source, methods, and display conventions. Human and mouse +assemblies (e.g. hg38, hg19, mm10, or mm39) will include tracks across nearly +all of these categories. However, most assemblies may only have a basic set of +annotations (genes, repeats, assembly mapping). + +Relevant FAQs: + +- [Gene Tracks](/FAQ/FAQgenes.html) +- [Genome Browser Tracks](/FAQ/FAQtracks.html) + + +## Visualizing Your Own Data + +The Genome Browser allows you to visualize your own data alongside the data we host: + +- [Custom tracks](/cgi-bin/hgCustom) + - See our [documentation](/goldenPath/help/customTrack.html) to learn how to load your own +- [Track hubs](/cgi-bin/hgHubConnect?#unlistedHubs) + - See our [Hubs Basics](/docs/hubs/hubBasics.html) page to create your hub + - Checked using our [hub development tools](/cgi-bin/hgHubConnect?#hubDeveloper) + +For both hubs and custom tracks, we provide storage through [hub space](/cgi-bin/hgHubConnect?#hubUpload). + +## Sharing Your Data + +Once you've loaded and configured your data, you can share it with others +through several means: + +- [Links](/FAQ/FAQlink.html) +- [Sessions](/cgi-bin/hgSession) +- [Public hubs](/cgi-bin/hgHubConnect?#publicHubs) (to contribute your own, see + our [guidelines](/goldenPath/help/publicHubGuidelines.html)) +- [Contributed tracks](/docs/hubs/contributedTracks.html) for GenArk assemblies + +Relevant FAQs: + +- [Data File Formats](/FAQ/FAQformat.html) - see the formats supported by the Genome Browser + + +## Downloading Data from the Genome Browser + +Beyond data visualization, the Genome Browser offers a wide variety of ways to access +and work with the underlying data: + +- The [download server](https://hgdownload.gi.ucsc.edu/downloads.html) provides + access to the data underlying the Genome Browser, + in addition to pairwise alignment and LiftOver chain files. +- Our [REST API](/goldenPath/help/api.html) can be used to retrieve data in JSON format. +- Our [public MySQL server](/goldenPath/help/mysql.html) allows command-line access to underlying data tables. +- We provide [command-line tools](https://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads) + for working with bigBed, bigWig, or other formats, + and command-line versions of our tools like `liftOver` or `blat`. + +We also provide scripts for creating your own +[mirror](/goldenPath/help/mirror.html) of the Genome Browser software and +databases, although it is often recommended to explore other methods of +visualizing your custom data as mirrors can require significant effort and +storage space to set up and maintain. + +Relevant FAQs: + +- [Data and Downloads](/FAQ/FAQdownloads.html) +- [Mirroring or Licensing the Genome Browser](/FAQ/FAQlicense.html)