6a211b4bfd69949866640e3c33054467c35b05cd jnavarr5 Wed May 8 09:40:11 2019 -0700 Adding another bigBedToBed example using the hgdownload-euro server, refs #20551 diff --git src/hg/htdocs/FAQ/FAQdownloads.html src/hg/htdocs/FAQ/FAQdownloads.html index dceb8f5..84298db 100755 --- src/hg/htdocs/FAQ/FAQdownloads.html +++ src/hg/htdocs/FAQ/FAQdownloads.html @@ -832,32 +832,42 @@ <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> <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, example:</p> +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: + <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> <strong>SNP data:</strong> If queries against the SNP table on one of our public MySQL servers or on your own MySQL installation are slow, then they can be sped up by using the "bin" field; you can <a href="../contacts.html">contact us</a> for more information.</p> <p> Read more in <a href="http://genome.ucsc.edu/blog/"> our blog</a> about <a href="http://genome.ucsc.edu/blog/?s=programmatic"> Accessing the Genome Browser Programmatically</a> to acquire data. </p> <a name="download37"></a> <h2>Obtaining GTF (Gene Transfer Format)</h2> <h6>What is the best method for obtaining GTF output?</h5> <p>