a7e37b9dfa1c8e2c3e135d08a8ee873a2e855d47 mspeir Mon Nov 3 16:47:06 2025 -0800 removing references to hgdownload-euro, refs #35031 diff --git src/hg/htdocs/FAQ/FAQdownloads.html src/hg/htdocs/FAQ/FAQdownloads.html index 1abecf9933f..cee9b1932a6 100755 --- src/hg/htdocs/FAQ/FAQdownloads.html +++ src/hg/htdocs/FAQ/FAQdownloads.html @@ -81,35 +81,34 @@ sequences from an assembly, see <a href="#download32">Extracting sequence in batch from an assembly</a>.</p> <p> For more information on using the UCSC DAS server, see <a href="#download23">Downloading data from the UCSC DAS server</a>.</p> <p> <p> Another option for querying sequence and annotation data is the <a href='../goldenPath/help/api.html' target=_blank>REST API</a>. This interface allows for extraction of sequence and annotations from both UCSC assemblies and from hubs.</p> <p> <strong>To quickly download large volumes of data you can use UDR (UDT Enabled Rysnc):</strong> UDR provides users much faster download rates. Here is an example using UDR, once installed, to download all the mouse mm9 ENCODE information that amounts to several terabytes:</p> <pre><code>$ udr rsync -avP hgdownload.gi.ucsc.edu::goldenPath/mm9/encodeDCC/ /my/local/mm9/</code></pre> -<pre><code>$ udr rsync -avP hgdownload-euro.soe.ucsc.edu::goldenPath/mm9/encodeDCC/ /my/local/mm9/</code></pre> <p> Optional: download from our secondary download server. -<pre><code>$ udr rsync -avP hgdownload2.soe.ucsc.edu::goldenPath/mm9/encodeDCC/ /my/local/mm9/</code></pre> +<pre><code>$ udr rsync -avP hgdownload2.gi.ucsc.edu::goldenPath/mm9/encodeDCC/ /my/local/mm9/</code></pre> Please read more about the new UDR method <a href="../../goldenPath/newsarch.html#030315" target="_blank">here</a>.</p> <a name="download35"></a> <h2>Metadata tables for GenBank and RefSeq moved to hgFixed database</h2> <h6>I can no longer find metadata tables like gbCdnaInfo for an assembly.</h6> <p> As of June 2016, the location of metadata tables that support the GenBank and RefSeq tracks (RefSeq, Other RefSeq, mRNA, EST, etc.) have been moved from directories of individual assemblies to one global database, hgFixed.</p> <p> The tables below (previously found per assembly) can now be downloaded from the <a href="http://hgdownload.gi.ucsc.edu/goldenPath/hgFixed/database/">hgFixed database</a>:</p> @@ -958,41 +957,37 @@ <h6>How do I access the data underlying a track?</h6> <p> The raw data underlying a track can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>, <a href="../cgi-bin/hgIntegrator">Data Integrator</a>, or <a href="../cgi-bin/hgVai">Variant Annotation Integrator</a>. For automated analysis, the genome annotation can be downloaded from the <a href="http://hgdownload.gi.ucsc.edu/">downloads server</a>, one of our two <a href="http://genome.ucsc.edu/goldenPath/help/mysql.html">public MariaDB servers</a>, or using our <a href='../goldenPath/help/api.html' target=_blank>REST API</a>.</p> <p> <strong>bigBed data:</strong> For <a href="FAQformat.html#format1.5">bigBed</a> files, individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="http://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can -also be used to obtain only features within a given range using one of the hgdownload servers, +also be used to obtain only features within a given range using our hgdownload server, example:</p> <ul> <li> North American server: <pre><code>bigBedToBed http://hgdownload.gi.ucsc.edu/gbdb/path/to/file/bigBedfile.bb -chrom=chr21 -start=0 -end=1000000 stdout </code></pre> </li> - <li> - European server: - <pre><code>bigBedToBed http://hgdownload-euro.soe.ucsc.edu/gbdb/path/to/file/bigBedfile.bb -chrom=chr21 -start=0 -end=1000000 stdout </code></pre> - </li> </ul> <p> Read more in <a href="https://genome-blog.gi.ucsc.edu/blog/"> our blog</a> about <a href="https://genome-blog.gi.ucsc.edu/blog/?s=programmatic">Accessing the Genome Browser Programmatically</a> to acquire data. </p> <p> <a name="snp"></a> <h2>How do I download dbSNP data?</h2> <p> For versions dbSNP153 and above, the data is formatted in bigBed files. Previous versions are MySQL tables. For help with versions before dbSNP153, see <a href="#download29">accessing MySQL data</a>. This FAQ entry pertains to versions dbSNP153 and above.</p> <p> Since dbSNP has grown to include over 700 million variants, the size of the All dbSNP (153+)