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/hgUnique.html src/hg/makeDb/trackDb/human/hs1/html/hgUnique.html
index 16ba2b6495d..33b7a16e744 100644
--- src/hg/makeDb/trackDb/human/hs1/html/hgUnique.html
+++ src/hg/makeDb/trackDb/human/hs1/html/hgUnique.html
@@ -1,45 +1,69 @@
 <h2>Description</h2>
 <p>These tracks show the regions unique to the T2T-CHM13 v2.0 assembly compared to the GRCh38/hg38 and GRCh37/hg19 reference assemblies.</p>
 
 
 <h2>Methods</h2>
 <p>
 <ul>
   
 <h3>Converting a chain file to the PAF format</h3>
 <p>We used the `to_paf.py` script from chaintools (https://doi.org/10.5281/zenodo.6342391, v0.1) to convert the v1_nfLO chains to the PAF format.</p>
 
 <h3>Obtaining unique regions</h3>
 <p>We used the follwing commands to obtain the regions unique to GRCh38/hg38 and GRCh37/hg19 in the BED format.</p>
   
 <pre><code>
 cut -f 1,3,4 grch38-chm13v2.paf  \
   | bedtools sort -i - -g chm13v2.0.fasta.fai \
   | bedtools merge \
   | bedtools complement -g chm13v2.0.fasta.fai -i - \
   | bedtools merge \
   > T2T-CHM13v2.0_unique_regions_hg38.bed
 
 cut -f 1,3,4 hg19-chm13v2.paf |  bedtools sort -i - -g chm13v2.0.fasta.fai \
   | bedtools merge \
   | bedtools complement -g chm13v2.0.fasta.fai -i - \
   | bedtools merge \
   > T2T-CHM13v2.0_unique__regions_hg19.bed
 </code></pre>
 
 </ul>
 </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>.</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/$db/hgUnique/" target="_blank">download server</a>.
+Individual regions or the whole genome annotation can be obtained using our tool
+<tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a precompiled
+binary for your system. Instructions for downloading source code and binaries can be found
+<a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>.
+The tool can also be used to obtain only features within a given range, for example:</p>
+<tt>bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/hgUnique/hgUnique.hg38.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>
 
 <p>
 The unique region annotations were generated by <a href="mailto:naechyun.chen@gmail.com">Nae-Chyun Chen&lt;naechyun.chen@gmail.com&gt;</a>
 and <a href="mvollger@uw.edu">Mitchell Vollger&lt;mvollger@uw.edu&gt;</a>
 </p>
 
 <h2>References</h2>
 
 <p>
 Nurk S, Koren S, Rhie A, Rautiainen M, et al. The complete sequence of a human genome. bioRxiv, 2021.
 </p>