7072384d5e6f4228bec4186d3d677527be0c9bc5 mspeir Fri Jun 26 09:37:20 2026 -0700 Adding data access to hs1 pages on the RR, refs # diff --git src/hg/makeDb/trackDb/human/hs1/html/sgdpCopyNumber.html src/hg/makeDb/trackDb/human/hs1/html/sgdpCopyNumber.html index 63999fceef1..49d96f39653 100644 --- src/hg/makeDb/trackDb/human/hs1/html/sgdpCopyNumber.html +++ src/hg/makeDb/trackDb/human/hs1/html/sgdpCopyNumber.html @@ -2,30 +2,54 @@ <html> <h3>Description</h3> This track represents copy number estimates form the <a href="https://www.simonsfoundation.org/simons-genome-diversity-project/"> Simons Genome Diversity Project</a>. Copy number is estimated over 500 bp windows of uniquely mappable sequence. Sequences are colored from cold to hot (0 - 120+) and exact copy can be found by clicking on the region of interest. <h3>Code Availability</h3> <a href="https://github.com/mrvollger/fastCN-smk">GitHub</a> <h3>Copy Number Key</h3> <table border="1"><tr><th>Copy number</th><th>Color</th></tr><tr><td style="text-align: center; vertical-align: middle;">0</td><td style="background: rgb(229,229,229); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(229,229,229)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">1</td><td style="background: rgb(196,196,196); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(196,196,196)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">2</td><td style="background: rgb(0,0,0); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(0,0,0)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">3</td><td style="background: rgb(0,0,205); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(0,0,205)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">4</td><td style="background: rgb(65,105,225); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(65,105,225)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">5</td><td style="background: rgb(100,149,237); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(100,149,237)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">6</td><td style="background: rgb(180,238,180); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(180,238,180)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">7</td><td style="background: rgb(255,255,0); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(255,255,0)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">8</td><td style="background: rgb(255,165,0); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(255,165,0)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">9</td><td style="background: rgb(139,26,26); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(139,26,26)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">10</td><td style="background: rgb(255,0,0); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(255,0,0)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">20</td><td style="background: rgb(0,255,255); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(0,255,255)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">30</td><td style="background: rgb(32,178,170); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(32,178,170)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">40</td><td style="background: rgb(0,255,0); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(0,255,0)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">50</td><td style="background: rgb(34,139,34); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(34,139,34)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">60</td><td style="background: rgb(0,100,0); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(0,100,0)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">70</td><td style="background: rgb(75,0,130); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(75,0,130)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">80</td><td style="background: rgb(139,0,139); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(139,0,139)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">90</td><td style="background: rgb(148,0,211); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(148,0,211)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">100</td><td style="background: rgb(199,21,133); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(199,21,133)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">110</td><td style="background: rgb(255,105,180); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(255,105,180)">■</div></td></tr><tr><td style="text-align: center; vertical-align: middle;">120</td><td style="background: rgb(255,192,203); text-align: center; vertical-align: middle;"><div style="font-size:15px; color:rgb(255,192,203)">■</div></td></tr></table> +<h3>Data Access</h3> +<p> +The raw data can be explored interactively with the +<a href="../cgi-bin/hgTables" target="_blank">Table Browser</a> or the +<a href="../cgi-bin/hgIntegrator" target="_blank">Data Integrator</a>. The data can also be +accessed from scripts through our <a href="https://api.genome.ucsc.edu" target="_blank">REST +API</a>.</p> +<p> +This track is a container of multiple subtracks; the underlying data are stored in bigBed files +that can be downloaded from our +<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/sgdpCopyNumber/" target="_blank">download server</a>. +Individual regions or the whole genome annotation can be obtained using our tool +<tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a precompiled +binary for your system. Instructions for downloading source code and binaries can be found +<a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>. +The tool can also be used to obtain only features within a given range, for example:</p> +<tt>bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/sgdpCopyNumber/LP6005441-DNA_A01_wssd.bb -chrom=chr6 -start=0 -end=1000000 stdout</tt> +<p> +Please refer to our +<a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome" target="_blank">mailing +list archives</a> for questions, or our +<a href="../FAQ/FAQdownloads.html#download36" target="_blank">Data Access FAQ</a> for more +information.</p> + <h3>Credits</h3> Please feel free to contact <a href=mailto:wharvey@uw.edu >William Harvey</a> or <a href=mailto:mvollger@uw.edu>Mitchell Vollger</a> with any questions and/or concerns regarding this track. <h3>References</h3> Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE. Recent segmental duplications in the human genome. Science 2002 <br><br> Pendleton AL, Shen F, Taravella AM, Emery S, Veeramah KR, Boyko AR, Kidd JM. Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication. BMC Biol. 2018 <br><br> Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, et al. Global diversity, population stratification, and selection of human copy-number variation. Science. 2015 <br><br> Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, et al. Diversity of human copy number. Science. 2010