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> + <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->