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/hs1PrimateChainNet.html src/hg/makeDb/trackDb/human/hs1/hs1PrimateChainNet.html
index b925065444c..99636787f57 100644
--- src/hg/makeDb/trackDb/human/hs1/hs1PrimateChainNet.html
+++ src/hg/makeDb/trackDb/human/hs1/hs1PrimateChainNet.html
@@ -131,30 +131,57 @@
 <em>netSyntenic</em> was used to fill in information about the relationship between
 higher- and lower-level chains, such as whether a lower-level
 chain was syntenic or inverted relative to the higher-level chain.
 The program <em>netClass</em> was then used to fill in how much of the gaps and chains
 contained <em>N</em>s (sequencing gaps) in one or both species and how much
 was filled with transposons inserted before and after the two organisms
 diverged.
 </p>
 
 <p>
 The resulting net file was converted to axt format via <em>netToAxt</em>,
 then converted to maf format via <em>axtToMaf</em>, then converted to
 the bigMaf format with <em>mafToBigMaf</em> and <em>bedToBigBed</em>
 </p>
 
+<h2>Data Access</h2>
+<p>
+The chains and alignments 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>
+For automated analysis, the underlying chain data are stored as bigChain files (one per query
+assembly) in the <tt>chainNet/</tt> directory on our
+<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/chainNet/" target="_blank">download server</a>.
+For chain tracks, individual regions or the whole genome annotation can be obtained using our tool
+<tt>bigChainToChain</tt>, while for net tracks, data can be accessed using the <tt>bigBedtoBed</tt>.
+Both tools can be compiled from the source code or downloaded as precompiled
+binaries 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>.
+Both tools can also be used to obtain only features within a given range, for example:</p>
+<tt>bigChainToChain https://hgdownload.soe.ucsc.edu/gbdb/hs1/chainNet/hs1.chainRBestGCA_028858775.2.bb -chrom=chr6 -start=0 -end=1000000 stdout</tt>
+<br>
+<tt>bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/hs1/chainNet/hs1.GCA_028858775.2.net.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>
 <em>lastz</em> was developed by Robert Harris, Pennsylvania State University.
 </p>
 <p>
 The <em>axtChain</em> program was developed at the University of California at
 Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</p>
 <p>
 The browser display and database storage of the chains and nets were created
 by Robert Baertsch and Jim Kent.</p>
 <p>
 The <em>chainNet</em>, <em>netSyntenic</em>, and <em>netClass</em> programs
 were developed at the University of California
 Santa Cruz by Jim Kent.</p>