7079fc959cca75f0b55651694407718866089320
lrnassar
  Fri Apr 8 17:58:37 2022 -0700
Swapping track order for clarity and prioritizing the liftOver track, refs #29203

diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html
index 81bdde0..4893761 100755
--- src/hg/htdocs/goldenPath/newsarch.html
+++ src/hg/htdocs/goldenPath/newsarch.html
@@ -150,37 +150,37 @@
 <b>Clinical annotations:</b>
 <ul>
 <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&c=CP068277.2&g=hub_3267197_clinVar20220313"
 target="_blank">ClinVar Variants</a> - Lifted ClinVar data from the hg38 March 13th, 2022 release.</li>
 <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&c=CP068277.2&g=hub_3267197_dbSNP155"
 target="_blank">dbSNP 155</a> - Lifted dbSNP 155 variants from the hg38 release.</li>
 <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&c=CP068277.2&g=hub_3267197_gwasSNPs2022-03-08"
 target="_blank">GWAS Variants</a> - GWAS catalog variants lifted from hg38.</li></ul></p>
 
 <p>
 <b>Comparative genomics:</b>
 <ul>
 <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&c=CP068277.2&g=hub_3267197_hgUnique"
 target="_blank">CHM13 unique</a> - Regions unique to the T2T-CHM13 v2.0 assembly as compared 
 to the hg38 and hg19 reference assemblies.</li>
+<li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&c=CP068277.2&g=hub_3267197_hgLiftOver"
+target="_blank">Human liftOver</a> - Contains one to one Nextflow LiftOver pipeline 
+alignments between CHM13 and hg19/hg38.</li>
 <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&c=CP068277.2&g=hub_3267197_GCA_009914755_4_T2T-CHM13v2_0ChainNet"
 target="_blank">Chain/Net Track</a> - Alignment track between CHM13 and four other human
 genomes that shows rearrangements in our usual chains (=alignable) and net (=synteny)
-display formats. Other genomes are hg19, hg38, HG002pat, and HG002mat.</li>
-<li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&c=CP068277.2&g=hub_3267197_hgLiftOver"
-target="_blank">Human liftOver</a> - Contains one to one Nextflow LiftOver pipeline 
-alignments between CHM13 and hg19/hg38.</li></ul></p>
+display formats. Other genomes are hg19, hg38, HG002pat, and HG002mat.</li></ul></p>
 
 <h3>How to display my data in CHM13i?</h3>
 <p>
 We have added support for CHM13 to our <a href="/cgi-bin/hgConvert?db=hg38&position=lastDbPos"
 target="_blank">hgConvert tool</a>. This allows region conversion of the current viewing 
 window between hg19/hg38 to CHM13 and vice versa. We will also be adding support for 
 conversion of data using our <a href="/cgi-bin/hgLiftOver" target="_blank">hgLiftOver tool</a> 
 at our next version release on May 3rd. In the meantime, the command line version of 
 <a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads"
 target="_blank">liftOver</a> in combination with the proper <a target="_blank"
 href="https://hgdownload.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/liftOver/">chain file</a>
 can be used to lift annotations.</p>
 
 <figure class="text-center">
 <img class='text-center' src="../images/hgConvert.png" width='80%' alt="Using hgConvert tool