78979d05311d0c6ea80313ef4b0861fce9d5ddc5 brianlee Wed Jul 6 11:57:51 2022 -0700 Code review changes refs #29706 diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html index 669993a..3d67b10 100755 --- src/hg/htdocs/goldenPath/help/hgTracksHelp.html +++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html @@ -627,102 +627,103 @@ To vertically reposition a track in the annotation track window, click-and-hold the mouse button on the side label, then drag the highlighted track up or down within the image. Release the mouse button when the track is in the desired position. To move an entire group of associated tracks (such as all the displayed subtracks in a composite track), click-and-hold the gray mini-button to the left of the tracks, then drag.</p> <a name="TRACK_CONFIG"></a> <h3>Viewing multiple regions</h3> <p> To remove intronic or intergenic regions from the display or to view only custom specified regions, click the <em>multi-region</em> button under the track image. For human assemblies hg17 and later, you may also replace a section of the reference genome with an alternate haplotype chromosome in order to view annotations upstream and downstream of the sequence. For more information about the multi-region feature see the <a href="./multiRegionHelp.html">multi-region help</a> page.</p> +<h3 id="config">Configuration panel</h3> <div class="text-center"> <a href ="/cgi-bin/hgTracks?hgTracksConfigPage=configure"> <img src="../../images/configureMenu.png" alt="Configuration menu options" width="700"> </a> </div> -<h3>Changing the width of the annotation track window</h3> +<h4>Changing the width of the annotation track window</h4> <p> The first time the annotation track window is displayed, or after the Genome Browser has been reset, the size of the track window is set by default to the width that best fits your Internet browser window. If you horizontally resize the browser window, you can automatically adjust the annotation track image size to the new width by clicking the <em>resize</em> button under the track image. To manually override the default width, enter a new value in the <em>image width</em> text box on the Track Configuration page, then click the <em>submit</em> button. The maximum supported width is 5000 pixels.</p> -<h3>Changing the width of the label area to the left of the image</h3> +<h4>Changing the width of the label area to the left of the image</h4> <p> The item labels (or track label, when viewed in dense mode) are displayed to the left of the annotation image. The width of this area is set to 17 characters by default. To change the width, edit the value in the <em>label area width</em> text box on the Track Configuration page, then click <em>Submit</em>.</p> -<h3>Changing the text size, font, in the annotation track image</h3> +<h4>Changing the text size, font, in the annotation track image</h4> <p> The annotation track image may be adjusted to display text in a range of fonts from AvantGarde, Courier, and Times. To change the size of the text, select an option from the <em>text size</em> pull-down menu on the Browser Configuration page, which you can find under the top blue "Genome Browser" menu by clicking <a target="_blank" href="/cgi-bin/hgTracks?hgTracksConfigPage=configure"><em>Configure</em></a>. Once you have made your selection, which can also include <em>style</em> click <em>submit</em>. The text size is set to "12" and "Helvetica" by default.</p> -<h3>Hiding the chromosome ideogram</h3> +<h4>Hiding the chromosome ideogram</h4> <p> The chromosome ideogram, located just above the annotation tracks image, provides a graphical overview of the features on the selected chromosome, including its bands, the position of the centromere, and an indication of the region currently displayed in the annotation tracks image. To hide the ideogram, uncheck the <em>Display chromosome ideogram above main graphic</em> box on the Tracks Configuration page.</p> -<h3>Hiding the light blue vertical guidelines</h3> +<h4>Hiding the light blue vertical guidelines</h4> <p> The light blue vertical guidelines on the annotation tracks image may be removed by unchecking the <em>Show light blue vertical guidelines</em> box on the Track Configuration page.</p> -<h3>Hiding the annotation track labels and description</h3> +<h4>Hiding the annotation track labels and description</h4> <p> The track and element labels displayed above and to the left of the tracks in the annotation tracks image may be hidden from view by unchecking the <em>Display track descriptions above each track</em> and <em>Display labels to the left of items in tracks</em> boxes, respectively, on the Track Configuration page.</p> -<h3 id="nextItem">Enabling next/previous item and exon navigation</h3> +<h4 id="nextItem">Enabling next/previous item and exon navigation</h4> +<div class="text-center"> + <a href ="/cgi-bin/hgTracks?db=hg38&position=chr10:67,881,992-67,890,592&hideTracks=1&knownGene=pack&omimAvSnp=pack&nextItemArrows=1"> + <img src="../../images/nextItem.png" alt="Ex. white/gray arrows for next/previous exon/item" width="700"></a> + <p class="gbsCaption text-center">Gray arrows jump to the next item, + while white arrows advance to the next exon.</p> +</div> <p> When the <em>Next/previous item navigation</em> configuration option is toggled on, on the Track Configuration page, gray double-headed arrows display in the Genome Browser tracks image on both sides of the track labels of gene, mRNA and EST tracks (or any standard tracks based on BED, PSL or genePred format). Clicking on the gray arrows shifts the image window toward that end of the chromosome so that the next item in the track is displayed. Similarly, the <em>Next/previous exon navigation</em> configuration option displays white double-headed arrows on the end of any item that extends off the edge of the current image. Clicking on one of the white arrows shifts the image window to the next exon in the indicated direction, unless the image window interrupts an exon, in which case the window shifts to the edge of the current exon. If the image window happens to be within a 5' or 3' UTR, then clicking the arrows shifts the image window towards the start or end of the next coding region, not the end of the exon.</p> -<div class="text-center"> - <a href ="/cgi-bin/hgTracks?db=hg38&position=chr10:67,881,992-67,890,592&hideTracks=1&knownGene=pack&omimAvSnp=pack&nextItemArrows=1"> - <img src="../../images/nextItem.png" alt="Ex. white/gray arrows for next/previous exon/item" width="700"></a> - <p class="gbsCaption text-center">Gray arrows jump to the next item, - while white arrows advance to the next exon.</p> -</div> <a name="RIGHT_CLICK_NAV"></a> <h3>Using the right-click navigation feature</h3> <p> Several of the common display and navigation operations offered on the Genome Browser tracks page may be quickly accessed by right-clicking on a feature on the tracks image and selecting an option from the displayed popup menu.</p> <div class="text-center"> <a target="_blank" href="/cgi-bin/hgTracks?db=hg38&position=chr21%3A31657975-31667213&hgt.reset=1&hgFind.matches=ENST00000270142.11&knownGene.show.noncoding=0&knownGene.show.spliceVariants=0"> <img src="../../images/right_click_example.png" alt="Example right-click to highlight a gene" width="700"> </a> </div> <p> Depending on context, the right-click feature allows the user to:</p> @@ -1249,32 +1250,32 @@ liftOver does not return a match if the region is split in the new assembly. Consider checking this option for conversions involving high-quality data within the same species. This option should not be used when mapping large regions, doing cross-species conversions or using fragmented poor-quality assemblies. <li><strong>Min ratio of alignment blocks/exons that must map</strong> (default 1)<strong>:</strong> <li><strong>If thickStart/thickEnd is not mapped, use the closest mapped bas</strong> (default off)<strong>:</strong> </ul> --> <h3>Command-line coordinate lifting</h3> <p> The command-line version of liftOver offers the increased flexibility and performance gained by -running the tool on your local server. See an example of running the liftOver tool -<a href="../../FAQ/FAQdownloads.html#liftOver">here</a>. +running the tool on your local server. See an example of +<a href="../../FAQ/FAQdownloads.html#liftOver">running the liftOver tool</a> on the command line. This utility requires access to a Linux platform. The executable file may be downloaded <a href="https://genome-store.ucsc.edu">here</a>. Command-line liftOver requires a UCSC-generated <em>over.chain</em> file as input. Pre-generated files for a given assembly can be accessed from the assembly's "LiftOver files" link on the <a href="http://hgdownload.soe.ucsc.edu/downloads.html">Downloads</a> page. If the desired conversion file is not listed, send a request to the <a href="../../contacts.html">genome mailing list</a> and we may be able to generate one for you. For use of the command-line version of LiftOver, we require all for-profit businesses or commercial companies to <a href="https://genome-store.ucsc.edu/">purchase a license</a> to support our small team.</p> <a name="Download"></a> <h2>Downloading genome data</h2> <p> Most of the underlying tables containing the genomic sequence and annotation data displayed in the Genome Browser can be downloaded. All of the tables are freely usable for any purpose except as