ee6aa4821b235509fa6827f7a7b29abe0f3a4862
mspeir
  Mon Feb 10 08:42:39 2025 -0800
minor tweaks to AlphaMissense description page, refs #32269

diff --git src/hg/makeDb/trackDb/human/alphaMissense.html src/hg/makeDb/trackDb/human/alphaMissense.html
index e1eb85d8839..316cb195b86 100644
--- src/hg/makeDb/trackDb/human/alphaMissense.html
+++ src/hg/makeDb/trackDb/human/alphaMissense.html
@@ -46,58 +46,58 @@
     <tr>
       <td>.565 - .340</td>
       <td style="color: rgb(192,192,192);">Likely Neutral</td>
     </tr>
     <tr>
       <td>&le; .340</td>
       <td style="color: rgb(80,166,230);">Likely Benign</td>
     </tr>
   </tbody>
 </table>
 
 
 <h2>Data access</h2>
 <p>
 AlphaMissense scores are available at the 
-<a href="https://sites.google.com/site/revelgenomics/" target="_blank">
+<a href="https://console.cloud.google.com/storage/browser/dm_alphamissense"
+target="_blank">
 AlphaMissense cloud storage site</a>.  
 The site provides precomputed AlphaMissense scores for all possible human missense variants 
 to facilitate the identification of pathogenic variants among the large number of 
 rare variants discovered in sequencing studies.
-
 </p>
 
 <p>
 The AlphaMissense data on the UCSC Genome Browser can be explored interactively with the
 <a href="../cgi-bin/hgTables">Table Browser</a> or the
-<a href="../cgi-bin/hgIntegrator">Data Integrator</a>. <br>
-For automated download and analysis, the genome annotation is stored at UCSC in bigWig
-files that can be downloaded from
-<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/alphaMissense/" target="_blank">our download server</a>.
-<br>
+<a href="../cgi-bin/hgIntegrator">Data Integrator</a>.
+</p>
+
+<p>
+For automated download and analysis, the genome annotation is stored at UCSC in
+<a href="../goldenPath/help/bigWig.html">bigWig</a> format that can be downloaded from
+<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/alphaMissense/"
+target="_blank">our download server</a>.
 The files for this track are called <tt>a.bw, c.bw, g.bw, t.bw</tt>. Individual
 regions or the whole genome annotation can be obtained using our tool <tt>bigWigToWig</tt>
 which can be compiled from the source code or downloaded as a precompiled
-binary for your system. <br>
-Instructions for downloading source code and binaries can be found
+binary for your system.  Instructions for downloading source code and binaries can be found
 <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>.
-<br>
-The tools can also be used to obtain features confined to given range, e.g.
-<br>&nbsp;
-<br>
+For example, to extract only annotations in a given region, you could use the following command:
+<p>
 <tt>bigWigToBedGraph -chrom=chr1 -start=100000 -end=100500 http://hgdownload.soe.ucsc.edu/gbdb/$db/alphaMissense/a.bw stdout</tt>
-<br>
+</p>
 
 <h2>Methods</h2>
 
 <p>
 Data were converted from the files provided on
 <a href="https://storage.cloud.google.com/dm_alphamissense"
 target = "_blank">the AlphaMissense Downloads website</a>. As with all other tracks,
 a full log of all commands used for the conversion is available in our 
 <a target=_blank href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/">source repository</a>, for <a target=_blank href="https://raw.githubusercontent.com/ucscGenomeBrowser/kent/master/src/hg/makeDb/doc/hg19.txt">hg19</a> and <a target=_blank href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/alphaMissense.txt">hg38</a>. The release used for each assembly is shown on the track description page.
 
 </p>
 
 <h2>Credits</h2>
 <p>
 Thanks to