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/hgLiftOver.html src/hg/makeDb/trackDb/human/hs1/html/hgLiftOver.html index 4637454c5a9..b09a164a5a4 100644 --- src/hg/makeDb/trackDb/human/hs1/html/hgLiftOver.html +++ src/hg/makeDb/trackDb/human/hs1/html/hgLiftOver.html @@ -112,30 +112,46 @@ uses dynamic programming and the CIGAR string to find an optimal splitting point between overlapping alignments in the query sequence. It starts its trimming with the largest overlap and then recursively trims smaller overlaps. </p> <p> Results were validated by using chaintools to confirm that there were no overlapping sequences with respect to both CHM13v2.0 and GRCh38 in the released chain file. In addition, trimmed alignments were visually inspected with SafFire to confirm their quality. </p> </ul> </p> +<h2>Data Access</h2> +<p> +The alignment 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>, and queried from scripts +through our <a href="https://api.genome.ucsc.edu" target="_blank">REST API</a>.</p> +<p> +The liftOver chain files used to convert coordinates between this assembly and GRCh38/hg38 or +GRCh37/hg19 are available for download in the <b>LiftOver chain file downloads</b> section above.</p> +<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 T2T v1_nflo liftOver chains were generated by <a href="mailto:naechyun.chen@gmail.com">Nae-Chyun Chen<naechyun.chen@gmail.com></a> and <a href="mvollger@uw.edu">Mitchell Vollger<mvollger@uw.edu></a>. The UCSC liftOver chains and the dot-plots were created by Hiram Clawson. </p> <p> <b>lastz</b> was developed by Robert Harris, Pennsylvania State University. </p> <p> The <b>axtChain</b> 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