eee0b1f73f5f01866f9e8b8dbb5ed153298d2638 lrnassar Wed May 15 14:53:53 2019 -0700 Linking to new hubAPI page from different FAQs #18869 diff --git src/hg/htdocs/FAQ/FAQdownloads.html src/hg/htdocs/FAQ/FAQdownloads.html index 9bd21be..8c470d3 100755 --- src/hg/htdocs/FAQ/FAQdownloads.html +++ src/hg/htdocs/FAQ/FAQdownloads.html @@ -65,30 +65,35 @@ 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 after a failure, when run again. Please see the previous link for examples.</p> <p> You can also download data from our <a href="http://hgdownload.soe.ucsc.edu/downloads.html">Downloads</a> page or our <a href="../cgi-bin/das/dsn" target="_blank">DAS server</a>. To download a specific subset of the data or to configure the output format of the data, use the <a href="../cgi-bin/hgTables">Table Browser</a>. For information on extracting a large set of 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>JSON 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.soe.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> 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 @@ -195,30 +200,33 @@ specifiers available for that assembly. The entry point specifies chromosome position, and the type indicates the annotation table requested. You can view the lists of entry points and types available for an assembly with requests of the form:</p> <pre><code>http://genome.ucsc.edu/cgi-bin/das/[db_name]/entry_points http://genome.ucsc.edu/cgi-bin/das/[db_name]/types </code></pre> <p> where [db_name] is the UCSC name for the assembly, e.g. hg16, mm4.</p> <p> For example, here is a query that returns all the records in the refGene table for the chromosome position chr1:1-100000 on the hg16 assembly: <pre><a href="../cgi-bin/das/hg16/features?segment=1:1,100000;type=refGene">http://genome.ucsc.edu/cgi-bin/das/hg16/features?segment=1:1,100000;type=refGene</a></pre> <p> For more information on DAS, see the <a href="http://www.biodas.org" target="_blank">Biodas website</a> and the <a href="http://www.biodas.org/documents/spec.html" target="_blank">DAS specification</a>.</p> +<p> +A more recent alternative to the DAS server is the <a href='../goldenPath/help/api.html' +target=_blank>JSON API</a>.</p> <a name="download27"></a> <h2>Downloading the UCSC Genome Browser source</h2> <h6>Where can I download the Genome Browser source code and executables?</h6> <p> The Genome Browser source code and executables are freely available for academic, nonprofit, and personal use (see <a href="FAQlicense.html#license2">Licensing the Genome Browser or Blat</a> for commercial licensing requirements). The latest version of the source code may be downloaded <a href="http://genome-store.ucsc.edu">here</a>.</p> <p> See <a href="FAQblat.html#blat3">Downloading Blat source and documentation</a> for information on Blat downloads.</p> <a name="download2"></a> <h2>Download restrictions</h2> @@ -825,32 +833,33 @@ browser (for more info see this <a href=FAQtracks.html#tracks1>FAQ</a>), but this start position listed in this section of the 4th column is actually 1 based. It will be the exact coordinate the feature starts on as displayed in the browser.</li> <li> Strand: forward(f) or reverse(-) strand.</li> </ul> <a name="download36"></a> <h2>Track Data Access</h2> <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.soe.ucsc.edu/">downloads server</a> or one of our two -<a href="http://genome.ucsc.edu/goldenPath/help/mysql.html">public MySQL servers</a>.</p> +<a href="http://hgdownload.soe.ucsc.edu/">downloads server</a>, one of our two +<a href="http://genome.ucsc.edu/goldenPath/help/mysql.html">public MySQL servers</a>, or +using our <a href='../goldenPath/help/api.html' target=_blank>JSON 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.soe.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, example:</p> <ul> <li> North American server: <pre><code>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/path/to/file/bigBedfile.bb -chrom=chr21 -start=0 -end=1000000 stdout </code></pre> </li> <li> European server: