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/sedefSegDups.html src/hg/makeDb/trackDb/human/hs1/html/sedefSegDups.html
index 6ea3c2425c5..3ac4de69c31 100644
--- src/hg/makeDb/trackDb/human/hs1/html/sedefSegDups.html
+++ src/hg/makeDb/trackDb/human/hs1/html/sedefSegDups.html
@@ -1,42 +1,66 @@
 <h2>Description</h2>
 A track showing segmental duplications as generated by <a href="https://github.com/vpc-ccg/sedef">sedef</a> on the assembly: T2T-CHM13-v2.0
 Column descriptions can be found here: <a href="https://github.com/vpc-ccg/sedef#output">columns</a>.
 
 <h2>Display Conventions and Configuration</h2>
 This section describes track configuration controls, or any special display conventions such as the
 meaning of different colors in your tracks. 
 
 <p>
 The following colors are used to distinguish levels of similarity:
 </p>
 <table>
   <tr><td>less than 90% similarity<td style="background-color:Purple; color:White">Purple</tr>
   <tr><td>90 - 98% similarity<td style="background-color:Gray; color:White">Light to dark gray</tr>
   <tr><td>98 - 99% similarity<td style="background-color:Yellow">Yellow</tr>
   <tr><td>greater than 99% similarity<td style="background-color:Orange">Orange</tr>
 </table>
 
 <h2>Methods</h2>
 <p>
 Sedef was run with default parameters on a RepeatMasked genome assembly.
 The resulting output (final.bed) was then converted into a browser friendly format (bed9 + extra fields).
 </p>
 
+<h2>Data Access</h2>
+<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>, where the track name is <tt>sedefSegDups</tt>.</p>
+<p>
+For automated analysis, the data may be downloaded from our
+<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/sedefSegDups/" target="_blank">download server</a> as a
+bigBed file. The file for this track is called <tt>sedefSegDups.bb</tt>. Individual regions or the whole
+genome annotation can be obtained using our tool <tt>bigBedToBed</tt>, which can be compiled from
+the source code or downloaded as a precompiled binary for your system. Instructions for downloading
+source code and binaries can be found
+<a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>.
+The tool can also be used to obtain only features within a given range, for example:</p>
+<tt>bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/sedefSegDups/sedefSegDups.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>
+
 <h2>Credits</h2>
 <ul>
   <li> <a href="mailto:mvollger@uw.edu"> Mitchell R. Vollger &lt;mvollger@uw.edu&gt;</a>, University of Washington
 </ul>
 
 <h2>References</h2>
 <p>
   M. R. Vollger et al., Segmental duplications and their variation in a complete
   human genome. Science. 2022 April 1; eabj6965. DOI: 10.1126/science.abj6965
 </p>
 Numanagic I, G&#246;kkaya AS, Zhang L, Berger B, Alkan C, Hach F.
 <a href="https://www.ncbi.nlm.nih.gov/pubmed/30423092" target="_blank">
 Fast characterization of segmental duplications in genome assemblies</a>.
 <em>Bioinformatics</em>. 2018 Sep 1;34(17):i706-i714.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30423092" target="_blank">30423092</a>;
 PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129265/" target="_blank">PMC6129265</a>
 </p>