80cbe376e37323c058df9ea964a567a4ac782343 brianlee Fri May 13 15:20:37 2022 -0700 Updating how to reset browser (after using WashU and not finding how to reset theirs) diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html index 179c4df..ad5f46c 100755 --- src/hg/htdocs/goldenPath/help/hgTracksHelp.html +++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html @@ -285,31 +285,31 @@ <p> The Genome Browser annotation tracks page displays a genome location specified through a Gateway search, a BLAT search, or an uploaded custom annotation track. There are five main features on this page: a set of <a href="#NAV">navigation controls</a>, a chromosome ideogram, the annotations tracks image, <a href="#TRACK_CONFIG">display configuration buttons</a>, and a set of track <a href="#TRACK_CONT">display controls</a>.</p> <p> The first time you open the Genome Browser, it will use the application default values to configure the annotation tracks display. By manipulating the navigation, configuration and display controls, you can customize the annotation tracks display to suit your needs. For a complete description of the annotation tracks available in all assembly versions supported by the Genome Browser, see the <a href="#IndivTracks"> Annotation Track Descriptions</a> section.</p> <p> The Genome Browser retains user preferences from session to session within the same web browser, although it never monitors or records user activities or submitted data. To restore the default -settings, click the "Click here to reset" link on the Genome Browser Gateway page. To +settings, click the "Reset All User Settings" under the top blue Genome Browser menu. To return the display to the default set of tracks (but retain custom tracks and other configured Genome Browser settings), click the <em>default tracks</em> button on the Genome Browser page.</p> <h3>Annotation track display conventions</h3> <p> <strong>Annotation track descriptions:</strong> Each annotation track has an associated description page that contains a discussion of the track, the methods used to create the annotation, the data sources and credits for the track, and (in some cases) filter and configuration options to fine-tune the information displayed in the track. To view the description page, click on the mini-button to the left of a displayed track or on the label for the track in the Track Controls section.</p> <p> <strong>Annotation track details pages:</strong> When an annotation track is displayed in full, pack, or squish mode, each line item within the track has an associated details page that can be displayed by clicking on the item or its label. The information contained in the details page @@ -504,32 +504,32 @@ establish a data threshold. By setting the min value to "50", only data values greater than 50 percent will display.</p> <p> To access filter and configuration options for a specific annotation track, open the track's description page by clicking the label for the track's control menu under the Track Controls section, the mini-button to the left of the displayed track, or the "Configure..." option from the Genome Browser's <a href="#RIGHT_CLICK_NAV">right-click</a> popup menu. The filter and configration section is located at the top of the description page. In most instances, more information about the configuration options is available within the description text or through a special help link located in the configuration section.</p> <p> Filter and configuration settings are persistent from session to session on the same web browser. To return the Genome Browser display to the default set of tracks (but retain custom tracks and other configured Genome Browser settings), click the <em>default tracks</em> button on the Genome Browser tracks page. To remove all user configuration settings and custom tracks, and completely -restore the defaults, click the "Click here to reset" link on the Genome Browser Gateway -page.</p> +restore the defaults, click the "Reset All User Settings" under the top blue Genome +Browser menu.</p> <h3> Video tutorial on changing track display modes</h3> <p><iframe width="560" height="315" src="https://www.youtube.com/embed/jKix2B3hwnw?rel=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe></p> <a name="NAV"></a> <h3>Zooming and scrolling the tracks display</h3> <p> At times you may want to adjust the amount of flanking region displayed in the annotation tracks window or adjust the scale of the display. At a scale of 1 pixel per base pair, the window accurately displays the width of exons and introns, and indicates the direction of transcription (using arrowheads) for multi-exon features. At a grosser scale, certain features - such as thin exons - may disappear. Also, some exons may falsely appear to fall within RepeatMasker features at some scales.</p>