5fb86269ebfbef64d7047b4943822ccd6f5365c0 galt Wed Jan 15 22:51:55 2025 -0800 More work to the new gb101 new docs page, refs #30335 diff --git docs/gb101.md docs/gb101.md index bb3e36e..9951b4e 100644 --- docs/gb101.md +++ docs/gb101.md @@ -1,313 +1,304 @@ -% Genome Browser Tutorials +% Introduction to the UCSC Genome Browser 101 -# Introduction to the UCSC Genome Browser +This tutorial is a basic introduction of the most common UCSC Genome Browser usage. This includes the +navigation menu, configuration of the tracks display, and where to find additional resources. -This page attempts to introduce you to the basics of using the UCSC Genome Browser including: - -- Basic Navigation -- Basic Table Browser Query -- Basic BLAT Query - -## Sections - -Use the sections below to learn about the UCSC Genome Browser interface. +Explore each of the three section below to learn the material in a different form. <div class="row" style="padding-top: 15px"> <div class="col-md-4"> <div class="panel panel-default" style="padding-bottom: 10px"> <h3 class="panel-title" style="width: -webkit-fill-available;" ->Genome Browser Interface</h3> +>Browser Interface Annotated Screenshot</h3> -Annotated screenshot of the Genome Browser interface. +This 'cheat sheet' highlights and describes the main features and functionalities of +the tracks display. <p style="text-align: end"> <button>[View](#annot-screenshot)</button> </p> </div> </div> <div class="col-md-4"> <div class="panel panel-default" style="padding-bottom: 10px"> <h3 class="panel-title" style="width: -webkit-fill-available;" >Guided Workthrough</h3> -Explains the basics of using/navigating the Genome Browser interface. +A guided workthrough that explains menu bar navigation, +as well as using and configuring the tracks display. <p style="text-align: end"> <button>[View](#guided-work)</button> </p> </div> </div> <div class="col-md-4"> <div class="panel panel-default" style="padding-bottom: 10px"> <h3 class="panel-title" style="width: -webkit-fill-available;" >Interactive Tutorial</h4> -Steps you through the basic functionality in the Genome Browser itself. - +An interactive tutorial that covers the basic Browser introduction on this page. <p style="text-align: end"> <button>[View](../cgi-bin/hgTracks?#showTutorial)</button> </p> </div> </div> </div> ## Annotated Screenshot ```image -src=../images/annot-screenshot-sarCov2.jpg -width=30% +src=../images/gb101cheatSheet.png +width=90% ``` - - -| Item | Explanation | -|------|-------------| -| Menu | Find BLAH | - -(We need something below the table otherwise later markdown isnt properly interpreted) - ## Guided Workthorugh -This walkthrough will take you through the basic Genome Browser functionality teaching you how to -turn on and off tracks, BLAH, and BLAH. - ### Navigating the Menus <!-- We are going to use bootstrap columns to put the image/text side by side Alternate the images left/right between different sections, mostly for aesthetics ---> <div class="row"> <div class="col-md-6"> -<img src="../images/GenomeSelect.jpg" alt="Genome selection" style="max-width:100%;"> +```image +src=../images/bluebarMenuGif.gif +width=70% +``` </div> <div class="col-md-6"> The navigation bar at the top of the page will allow you to access our tools, downloads, and help pages. There are five main drop-downs that are useful for most users: - Genomes - switch between the many genomes available. - Genome Browser - configure, search for tracks, and reset the Genome Browser back to the default settings. - Tools - access to features such as [BLAT](../cgi-bin/hgBlat), [isPCR](../cgi-bin/hgPcr), and [LiftOver](../cgi-bin/hgLiftOver). The [Table Browser](../cgi-bin/hgTables) can also export track data in various file formats. - My Data - create stable short links ([Sessions](../cgi-bin/hgSession)) and visualize your own data via [custom tracks](../cgi-bin/hgCustom) or [track hubs](../cgi-bin/hgHubConnect). - Help - access contact information, FAQs, and Browser Documentation. </div> </div> ### Using the Search Box <div class="row"> <div class="col-md-6"> The search bar allows you to navigate to a region on the genome using [genome coordinates](https://genome-blog.soe.ucsc.edu/blog/2016/12/12/the-ucsc-genome-browser-coordinate-counting-systems/), [gene symbols](https://genome.ucsc.edu/FAQ/FAQgenes.html#genename), [rsIDs](https://www.ncbi.nlm.nih.gov/snp/docs/RefSNP_about/#what-is-a-reference-snp), [HGVS](http://varnomen.hgvs.org/) terms, or DNA sequence. You can even search documentation and FAQ pages using this search bar. A few example queries are: - chr1:127140001-127140001 - SOD1 - rs2569190 - NM_198056.3:c.1654G>T - CCTTCCTATAGTCCGGAATACGCC AATGGCGCGGCCGGCCTGGACC ACTCCCATTACGGGGGTGTCCC GGGCAGCGGGGCCGGAGGCTTA ATGCAAAGGC Please note, [BLAT](https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign) is used if your search term is a DNA sequence. For the best results, make sure your sequence is long enough to meet BLAT specifications. The [examples](https://genome.ucsc.edu/goldenPath/help/query.html) link next to the search bar contains even more search queries. </div> <div class="col-md-6"> <img src="../images/GeneSearch.jpg" alt="Genome selection" style="max-width:100%;"> </div> </div> ### Highlights and Zooming <div class="row"> <div class="col-md-6"> -<!-- -<img> here ---> +```image +src=../images/highlightZoomGif.gif +width=100% +``` </div> <div class="col-md-6"> Dragging the Genome Browser image performs different tasks depending on where and how you click the image. Click-and-Drag the ruler at the top of the image will bring up a menu to zoom into or highlight the region. Click-and-Drag anywhere else on the Genome Browser image to scroll to the left or right. Alternatively, you can: - Hold **Alt+drag** or **Option+drag** to highlight - Hold **Ctrl+drag** or **Cmd+drag** to zoom </div> </div> ### Configuring Data Track Display <div class="row"> <div class="col-md-6"> Clicking on the rectangle box next to a track is an easy way to go to that track's settings page quickly. [Right-clicking](../goldenPath/help/hgTracksHelp.html#RIGHT_CLICK_NAV) on the track will also bring up a menu to change the display mode, configure a track, or view a PNG image of the current window. </div> <div class="col-md-6"> -<!-- -<img> here ---> +```image +src=../images/rightClickAndGreyBarGif.gif +width=95% +``` </div> </div> ### Track Display Modes <div class="row"> <div class="col-md-6"> <!-- <img> here --> </div> <div class="col-md-6"> Annotation tracks can be entirely hidden or shown in four different ways that take an increasing amount of vertical space: [dense, squish, pack, and full](../goldenPath/help/hgTracksHelp.html#TRACK_CONT). *Pack display is the recommended visibility for most data types as it provides the best balance of information and space.* After changing a track's display mode, the change will not be applied until you refresh the page. You can either refresh the page manually using your web browser or click <button>refresh</button> on any of the track groups. </div> </div> ### Searching for Data Tracks <div class="row"> <div class="col-md-6"> Having trouble finding a dataset for your genome assembly? The [Track Search](../cgi-bin/hgTracks?hgt_tSearch=track+search) feature allows searching for terms in track names, descriptions, groups, and ENCODE metadata. More information about <button>track search</button> can be found on the following [help page](../goldenPath/help/trackSearch.html). The Track Search feature can also be accessed by hovering over the "Genome Browser" drop-down menu. </div> <div class="col-md-6"> <!-- <img> here --> </div> </div> ### Configuring the Genome Browser Display <div class="row"> <div class="col-md-6"> -<!-- -<img> here ---> +```image +src=../images/configureGif.gif +width=90% +``` </div> <div class="col-md-6"> Use the <button>configure</button> button to customize graphic font, size, gridlines, and more. This can be helpful when exporting an image for publication. You can also find a link to configure the browser image by hovering over the "Genome Browser" drop-down menu. </div> </div> ### Viewing the Reverse Strand <div class="row"> <div class="col-md-6"> By default, the UCSC Genome Browser displays the forward strand (5' to 3') but can be configured to display the negative strand (3' to 5'). To reverse the genome orientation, click the <button>reverse</button> button, and the Genome Browser image will flip to show either the negative or positive strand. </div> <div class="col-md-6"> -<!-- -<img> here ---> +```image +src=../images/reverseStrand.png +width=90% +``` </div> </div> ### Getting Help Using the Genome Browser <div class="row"> <div class="col-md-6"> -<!-- -<img> here ---> +```image +src=../images/gettingHelp.png +width=40% +``` </div> <div class="col-md-6"> The [training page](../training/) has other guides and training videos. You can also search the [mailing list archive](https://groups.google.com/a/soe.ucsc.edu/g/genome) for previously answered questions. If you still have questions after searching the [FAQ page](../FAQ/) or [Genome Browser User Guide](../goldenPath/help/hgTracksHelp.html) pages, you can email the suitable mailing list for your inquiry from the [Contact Us](../contacts.html) page. Follow our [citation guidelines](../cite.html) when using the Genome Browser tool suite or data from the UCSC Genome Browser database in a research work that will be published in a journal or on the Internet. In addition to the [relevant paper](goldenPath/pubs.html), please reference the Genome Browser website in your manuscript: *http://genome.ucsc.edu*. </div> </div>