bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/bigChain.html src/hg/htdocs/goldenPath/help/bigChain.html index 21b28bc0e6b..d1fba62c819 100755 --- src/hg/htdocs/goldenPath/help/bigChain.html +++ src/hg/htdocs/goldenPath/help/bigChain.html @@ -59,48 +59,48 @@ <p> To create a bigChain track, follow these steps:</p> <p> <strong>Step 1.</strong> If you already have a chain file you would like to convert to a bigChain, skip to <em>Step 3</em>. Otherwise download <a href="examples/chr22_KI270731v1_random.hg38.mm10.rbest.chain">this example chain file</a> for the human GRCh38 (hg38) assembly.</p> <p> <strong>Step 2.</strong> Download these autoSql files needed by <code>bedToBigBed</code>: <em><a href="examples/bigChain.as">bigChain.as</a></em> and <em><a href="examples/bigLink.as">bigLink.as</a></em>.</p> <p> <strong>Step 3.</strong> Download the <code>bedToBigBed</code> and <code>chainToBigChain</code> programs from the UCSC -<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">binary utilities directory</a>.</p> +<a href="http://hgdownload.gi.ucsc.edu/admin/exe/">binary utilities directory</a>.</p> <p> <strong>Step 4.</strong> Use the <code>fetchChromSizes</code> script from the -<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">same directory</a> to create a +<a href="http://hgdownload.gi.ucsc.edu/admin/exe/">same directory</a> to create a <em>chrom.sizes</em> file for the UCSC database with which you are working (e.g., hg38). Alternatively, you can download the <em>chrom.sizes</em> file for any assembly hosted at UCSC from our -<a href="http://hgdownload.soe.ucsc.edu/downloads.html">downloads</a> page (click on "Full +<a href="http://hgdownload.gi.ucsc.edu/downloads.html">downloads</a> page (click on "Full data set" for any assembly). For example, the <em>hg38.chrom.sizes</em> file for the hg38 database is located at -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes" -target="_blank">http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes</a>.</p> +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes" +target="_blank">http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes</a>.</p> <p> Here are wget commands to obtain these above files. <pre><code>wget https://genome.ucsc.edu/goldenPath/help/examples/bigChain.as wget https://genome.ucsc.edu/goldenPath/help/examples/bigLink.as -wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes +wget http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes wget https://genome.ucsc.edu/goldenPath/help/examples/chr22_KI270731v1_random.hg38.mm10.rbest.chain </code></pre></p> <p> <strong>Step 5.</strong> Use the <code>chainToBigChain</code> utility to generate the pre-bigChain and pre-bigLink files:</p> <pre><code>chainToBigChain chr22_KI270731v1_random.hg38.mm10.rbest.chain bigChain.pre bigChain.link.pre</code></pre> <p> <strong>Step 6.</strong> Create the bigChain and bigLink files using the <code>bedToBigBed</code> utility: <pre><code>bedToBigBed -type=bed6+6 -as=bigChain.as -tab bigChain.pre hg38.chrom.sizes bigChain.bb bedToBigBed -type=bed4+1 -as=bigLink.as -tab bigChain.link.pre hg38.chrom.sizes bigChain.link.bb </code></pre></p> <p> <strong>Step 7.</strong> Move the newly created bigChain (<em>bigChain.bb</em>) and bigLink (<em>bigChain.link.bb</em>) @@ -151,64 +151,64 @@ to that which is available for a standard chain track.</p> <h3>Example #2</h3> <p> In this example, you will create your own bigChain file from an existing chain input file.</p> <ol> <li> Save <a href="examples/chr22_KI270731v1_random.hg38.mm10.rbest.chain">this chain file</a> to your computer (<em>Step 1</em> in <em>Creating a bigChain track</em>, above).</li> <li> Save the autoSql files <a href="examples/bigChain.as"><em>bigChain.as</em></a> and <a href="examples/bigLink.as"><em>bigLink.as</em></a> to your computer (<em>Step 2</em>, above).</li> <li> Download the <code>bedToBigBed</code> and <code>chainToBigChain</code> - <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">utilities</a> (<em>Step 3</em>, above).</li> + <a href="http://hgdownload.gi.ucsc.edu/admin/exe/">utilities</a> (<em>Step 3</em>, above).</li> <li> Save the <a href="hg38.chrom.sizes"><em>hg38.chrom.sizes</em> text file</a> to your computer. This file contains the chrom.sizes for the human hg38 assembly (<em>Step 4</em>, above).</li> <li> Run the utilities in <em>Steps 5-7</em>, above, to create the bigChain and bigLink output files. </li> <li> Place the newly created bigChain (<em>bigChain.bb</em>) and and bigLink (<em>bigChain.link.bb</em>) files on a web-accessible server (<em>Step 8</em>).</li> <li> Construct a track line that points to the bigChain file (<em>Step 9</em>, above).</li> <li> Create the custom track on the human assembly hg38 (Dec. 2013), and view it in the Genome Browser (<em>Step 10</em>, above).</li> </ol> <h2>Sharing your data with others</h2> <p> If you would like to share your bigChain data track with a colleague, learn how to create a URL by looking at Example 6 on <a href="customTrack.html#EXAMPLE6">this page</a>.</p> <h2>Extracting data from the bigChain format</h2> <p> Because the bigChain files are an extension of bigBed files, which are indexed binary files, it can be difficult to extract data from them. UCSC has developed the following programs to assist in working with bigBed formats, available from the -<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">binary utilities directory</a>.</p> +<a href="http://hgdownload.gi.ucsc.edu/admin/exe/">binary utilities directory</a>.</p> <ul> <li> <code>bigBedToBed</code> — converts a bigBed file to ASCII BED format.</li> <li> <code>bigBedSummary</code> — extracts summary information from a bigBed file.</li> <li> <code>bigBedInfo</code> — prints out information about a bigBed file.</li> </ul> <p> As with all UCSC Genome Browser programs, simply type the program name (with no parameters) at the command line to view the usage statement.</p> <h2>Troubleshooting</h2> <p> If you encounter an error when you run the <code>bedToBigBed</code> program, check your input file for data coordinates that extend past the the end of the chromosome. If these are present, run the <code>bedClip</code> program -(<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">available here</a>) to remove the problematic +(<a href="http://hgdownload.gi.ucsc.edu/admin/exe/">available here</a>) to remove the problematic row(s) in your input file before running the <code>bedToBigBed</code> program.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->