10bb49ac599fb3b14966b832cc4992673db5394f kuhn Wed Sep 8 22:35:27 2021 -0700 added links to vids on the page from within text sections diff --git src/hg/htdocs/goldenPath/help/multiRegionHelp.html src/hg/htdocs/goldenPath/help/multiRegionHelp.html index 8b1a6a3..0ca7775 100755 --- src/hg/htdocs/goldenPath/help/multiRegionHelp.html +++ src/hg/htdocs/goldenPath/help/multiRegionHelp.html @@ -136,30 +136,34 @@ <p> The exon-only view "virtual chromosome" is constructed of all the exons present in the gene track specified in the multi-region configuration window. Exon "slices" are visually separated by blocks of intronic or intergenic bases, the size of which are set by the padding field. This designates the padding on both sides of an exon, and therefore is additive, e.g., a padding size of 6 will result in a 12-base space between exon slices:</p> <p> <img src="../../images/MultiRegionExonPadding.png" alt="Multi-Region padding" width="950" height="171"> </p> <p> If the gene track used to compute the slicing is a <a href="./trackDb/trackDbDoc.html#superTrack">super track</a> or contains other transcripts, only the longest exon will be used to determine slicing, regardless of whether or not they are in the same transcript. See <a href="#Example1">Example 1</a> for more information. +<p> +<a href ="#ExonOnlyVid">Video</a> +</p> + <a name="GeneOnly"></a> <h3>Gene-only mode</h3> <p> The gene-only view displays the bases and annotations that fall within the coordinates of a gene, but hides all of the intergenic bases except those used for padding (<a href="#Example2">Example 2</a>). As with exon-only mode, the padding field sets the number of intergenic bases displayed to visually separate each gene slice.</p> <p> Because genes and alternate transcripts often overlap by a few bases, the windows created by the gene-only (and exon-only) mode may sometimes merge together. Reducing the number of padding bases may increase the number of alternate regions by allowing less intergenic space between genes. However, this overlap is a common feature for most of the Genome Browser gene sets, and should be no cause for concern.</p> <a name="CustomRegions"></a> @@ -208,46 +212,53 @@ will display a message asking if you would like to return to a default view at that location. If you prefer to return to your custom region instead, click <button type="button">OK</button>. Otherwise, click "here" to return to the default view. </p> <p> <img src="../../images/MultiRegionBEDSearchRedirectMessage.png" alt="Multi-Region search redirect" width="691" height="97"></p> <p> If the term is not found at all in the assembly, an error message will display.</p> <p> When scrolling or zooming while viewing regions from a custom BED URL, the range is restricted to the BED-defined regions. Although you can still zoom in to single base resolution, the outward zoom is limited to the extent of the defined regions. Scrolling upstream and downstream is also limited to the BED-defined range.</p> +<p> +<a href ="#CustomRegionsVid">Video</a> +</p> + <a name="Haplotype"></a> <h3>Haplotype mode</h3> <p> An additional viewing mode is available on human assemblies hg17 and later: showing an alternative haplotype placed in its chromosomal context (<a href="#Example5">Example 5</a>). The haplotype is specified by entering its ID in the form <em>chr_name_alt</em> in the configuration window. To view the list of haplotype IDs for a given assembly, go to <code>http://hgdownload.soe.ucsc.edu/goldenPath/<strong>$db</strong>/bigZips/<strong>$db</strong> .chrom.sizes</code>, where <strong><code>$db</code></strong> is the human assembly name (e.g., hg38, hg19, hg18 or hg17).</p> <p> Alternatively, haplotypes can be viewed using the <strong>Alt Map...</strong> track in the Mapping and Sequencing group. Open the track and navigate to the haplotype of interest in the track window. Click on the haplotype to display its details page, then click the link <strong>Show this alternate haplotype placed on its chromosome</strong>.</p> +<p> +<a href ="#HaplotypeVid">Video</a> +</p> <a name="Videos"></a> <p> </p> <h2>Videos</h2> <a name="ExonOnlyVid"></a> <p> </p> <h3>Video demonstration of Exon-only mode</h3> <p> </p><p> <iframe width="560" height="315" src="https://www.youtube.com/embed/mNEJBOkf_Gk?rel=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture"