481dd77123df9a0bd00a6dedb595bbcf6546f3e7
gperez2
  Wed Apr 12 18:04:06 2023 -0700
Adding FAQ for differences in conservation scores between download file and hgTracks/hgTables, refs #30734

diff --git src/hg/htdocs/FAQ/FAQdownloads.html src/hg/htdocs/FAQ/FAQdownloads.html
index a5c3da2..08a4673 100755
--- src/hg/htdocs/FAQ/FAQdownloads.html
+++ src/hg/htdocs/FAQ/FAQdownloads.html
@@ -41,30 +41,31 @@
 <li><a href="#download19">Data from Evolutionary Conservation Score tracks</a></li>
 <li><a href="#download20">Minus strand coordinates - axtNet files</a></li>
 <li><a href="#download21">Mapping UCSC STS marker IDS to those of other groups</a></li>
 <li><a href="#download22">deCODE map data</a></li>
 <li><a href="#download29">Direct MariaDB (MySQL) access to data</a></li>
 <li><a href="#download34">Name of fourth column in BED output</a></li>
 <li><a href="#download36">Track data access</a></li>
 <li><a href="#snp">How do I download dbSNP data?</a></li>
 <li><a href="#snpAlleles">Why doesn't this SNP have two alleles?</a></li>
 <li><a href="#download37">Known issues with Table Browser GTF output</a></li>
 <li><a href="#download38">Table Browser output file not ordered</a></li>
 <li><a href="#download39">'Permisssion denied' error when trying to use command-line utilities</a></li>
 <li><a href="#download40">Restricted Track Data</a></li>
 <li><a href="#downloadAnalysis">What is the genome analysis set?</a></li>
 <li><a href="#downloadGenArk">How do I download GenArk data?</li>
+<li><a href="#downloadConservation">Why are the conservation scores different from the ones in the download file?</li>
 </ul>
 <hr>
 <p>
 <a href="index.html">Return to FAQ Table of Contents</a></p>
 
 <a name="download1"></a>
 <h2>Downloading sequence and annotation data</h2>
 <h6>How do I obtain the sequence and/or annotation data for a release?</h6>
 <p> 
 Sequence and annotation data downloads are usually made available within the first week of the 
 release of a new assembly. The download directories are automatically updated nightly to 
 incorporate additions and modifications to the data.</p> 
 <p>
 You can download sequence and annotation data <a href="../goldenPath/help/ftp.html">using our FTP 
 server</a>, but we recommend using rsync, which has the advantage of starting up where it left off 
@@ -1206,16 +1207,28 @@
 than our goldenPath, SQL, or gbdb file directories. There are two ways to access 
 this data for download. First, you can go to the 
 <a href="https://hgdownload.soe.ucsc.edu/hubs">GenArk page</a>
 and select your clade (primates, mammals, birds, etc.) and then
 you will be brought to a page with a table of species and 
 GCA/GCF assembly identifiers. Find your genome and click on the third column, 
 labeled "Scientific name and data download", which will take you to the download 
 directory for that species. 
 </p><p>
 Alternatively, you can enter your GCA/GCF identifier 
 in the URL in groups of three characters, seperated by slashes. For example, the 
 identifier "GCA_004027835.1" has data in the following directory:
 <pre>https://hgdownload.soe.ucsc.edu/hubs/GCA/004/027/835/</pre>
 </p>
 
+<a name="downloadConservation"></a>
+<h2>Conservation scores downloads</h2>
+<h6>Why are the conservation scores on the UCSC Genome Browser site different from the ones in the
+download file?</h6>
+<p>
+The difference in the conservation scores, for both PhastCons and PhyloP, is that the wiggle
+database format (from which the details page and Table Browser scores are extracted) uses lossy
+compression that keeps enough resolution to display the pixelated scores in the browser graphic
+display but does not reconstruct the true original scores. This is why we make the original score
+files available for download.
+</p>
+
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