d3bc7aa1bb4f8066f800ac7286d8d995292f3fa7 gperez2 Wed Nov 8 09:37:31 2023 -0800 Announcing the new track decorators feature, refs #32467 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index fd1262d..5d1748f 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,82 @@ </div> <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>our GitHub page</a>.</p> <!-- ============= 2023 archived news ============= --> <a name="2023"></a> +<a name="110823"></a> +<h2>Nov. 08, 2023 New track decorators feature</h2> +<p> +We are excited to introduce the new track decorators feature which allows highlighting parts of +features with colors and/or symbols (glyphs/shapes) within a single track. +</p> +<div class="text-center"> + <a href="http://genome.ucsc.edu/s/gperez2/RM_32467" target="_blank"> + <img src="/images/newsArchImages/feature_decorators.png" style="width:80%;max-width:1083px"></a> +</div> +<p> +The genome browser‘s primary way to annotate the genome uses colored rectangles +(“exons” for gene tracks) linked by thin lines (“introns”), often stored +as a bigBed. These were originally used for genes but then evolved to cover other types of +annotations, e.g. enhancers, chromatin modifications, or single nucleotide variants. We usually +call these annotations “features”. Each rectangle (“exon”) of a feature has +the same color and individual parts cannot be highlighted. If you wanted to highlight parts of the +features, traditionally this required a second track. +</p> +<div class="text-center"> + <img src="../../images/runx2.png" style="width:80%;max-width:1083px"> +</div> +<p> +Track decorators change this: in your custom track and track hubs, you can now highlight parts of a +genome annotation with colors or symbols. Track decorators can be shown in two styles, +“block” and “glyph” style, and can either be overlaid onto the feature or +shown directly underneath. The “block” style option can be used to color exons and +introns and can display a label for them. For example, the “block” track decorator +could be used to overlay protein domain boundaries on transcripts where usually one would use an +entirely different track for the domains. +</p> +<div class="text-center"> + <img src="../../images/runx2_decorator.png" style="width:80%;max-width:1083px"> +</div> +<p> +The “glyph” style option offers 8 different types of glyphs and the color of choice. +</p> +<div class="text-center"> + <img src="../../images/glyphsEx.png" style="width:40%;max-width:1083px"> +</div> +<p> +The “glyph” style option can be used to draw entirely new symbols, for example, to +indicate insertion positions on the genome with small triangles. For more information, see the +<a href="/goldenPath/help/decorator.html" target="_blank">Track Decorators help page</a></p> +<p> +We would like to thank Jonathan Casper, Max Haeussler, Mark Diekhans, and Gerardo Perez for their +work on this release. We appreciate user feedback. If you have questions, feedback, suggestions, +glyph style requests, or have found new glyph applications, please contact our +<a href="mailto:genome@soe.ucsc.edu">mailing list</a>. +We would appreciate responses on the creative ways of using the new track decorators feature. +</p> + <a name="102323"></a> <h2>Oct. 23, 2023 eMERGE polygenic risk scores for human (hg19)</h2> <p> We are pleased to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=prsEmerge">eMerge polygenic risk scores</a> for the human assembly GRCh37/hg19. Polygenic risk scores (PRS) have clinical utility and are the result of many years of GWAS studies. A score is given for a combination of SNPs to calculate the risk of getting a disease in a healthy population. These scores work very well for cancer, cardiomyopathies, and is extending to other diseases. </p> <p> The Polygenic Risk Scores eMERGE track shows variants that are part of selected polygenic risk scores for 8 common diseases. The risk scores were selected by the <a href="https://www.genome.gov/Funded-Programs-Projects/Electronic-Medical-Records-and-Genomics-Network-eMERGE" target="_blank">NHGRI eMERGE project</a>, and the selection process is described in