fdfd2f7808d5ca212f9433e5f941b9aba74f07af lrnassar Tue Mar 31 16:12:39 2026 -0700 Small tweaks to new browser docs intro page, refs #36894 diff --git docs/index.md docs/index.md index d7144ff96e1..3eb4b13c80a 100644 --- docs/index.md +++ docs/index.md @@ -1,21 +1,19 @@ --- title: "Genome Browser Documentation" --- -Browse all UCSC Genome Browser documentation by topic. - 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. ## Using the Genome Browser Interface and Tools 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. ### Tutorials We offer detailed step-by-step tutorials for several of our tools: @@ -24,32 +22,32 @@ | 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 +The Genome Browser allows for the visualization of annotations on +a 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