bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/bigPsl.html src/hg/htdocs/goldenPath/help/bigPsl.html index 2fbcabf0a89..a62e747ccc4 100755 --- src/hg/htdocs/goldenPath/help/bigPsl.html +++ src/hg/htdocs/goldenPath/help/bigPsl.html @@ -93,42 +93,42 @@ <h2>Creating a bigPsl track</h2> <p> To create a bigPsl track, follow these steps:</p> <p> <strong>Step 1.</strong> If you already have a PSL file created using BLAT or another tool, skip to <em>Step 2</em>. Otherwise, download the example PSL file <a href="examples/bigPsl.psl"><em>bigPsl.psl</em></a> for the human GRCh38/hg38 assembly. You will also want to download the files <a href="examples/bigPsl.fa"><em>bigPsl.fa</em></a> and <a href="examples/bigPsl.cds"><em>bigPsl.cds</em></a> if you would like to use the alternate options described in <em>Step 4</em>, below.</p> <p> <strong>Step 2.</strong> Download the <code>bedToBigBed</code> and <code>pslToBigPsl</code> programs 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> <p> <strong>Step 3.</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 +our <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> <strong>Step 4.</strong> Use the <code>pslToBigPsl</code> utility to create a bigPsl file in bed12+13 format that contains the 25 fields described in the bigPsl format definition <a href="#bigPsl">above</a>. The file must include the 13 extra fields: <code>oChromStart</code>, <code>oChromEnd</code>, <code>oStrand</code>, <code>oChromSize</code>, <code>oChromStarts</code>, <code>oSequence</code>, <code>oCDS</code>, <code>chromSize</code>, <code>match</code>, <code>misMatch</code>, <code>repMatch</code>, <code>nCount</code>, and <code>seqType</code>.</p> <pre><code>pslToBigPsl bigPsl.psl stdout | sort -k1,1 -k2,2n > bigPsl.txt</code></pre> <p> If you are using your own PSL file, you may have corresponding FASTA and CDS files that accompany it. You can provide these files as input to <code>pslToBigPsl</code> to generate a more informative bigPsl file:</p> <pre><code>pslToBigPsl bigPsl.psl -cds=bigPsl.cds -fa=bigPsl.fa stdout | sort -k1,1 -k2,2n > bigPsl.txt</code></pre> <p> @@ -183,68 +183,68 @@ <p> After this example bigPsl is loaded in the Genome Browser, click on a track item in the Genome Browser's track display. Note that the details page displays information about the alignment, similar that which is available for PSL tracks, as well as links that display the browser position of the alignment and other detailed information about the alignment.</p> <h2>Example #2</h2> <p> In this example, you will create your own bigPsl file from an existing bigPsl input file.</p> <ol> <li> Save the example bed12+13 file <a href="examples/bigPsl.txt"><em>bigPsl.txt</em></a> to your computer (<em>Step 4</em> in <em>Creating a bigPsl track</em>, above</em>).</li> <li> Download the - <a href="http://hgdownload.soe.ucsc.edu/admin/exe/"><code>bedToBigBed</code> utility</a> + <a href="http://hgdownload.gi.ucsc.edu/admin/exe/"><code>bedToBigBed</code> utility</a> (<em>Step 2</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 3</em>, above).</li> <li> Save the autoSql file <a href="examples/bigPsl.as"><em>bigPsl.as</em></a> to your computer.</li> <li> Run the <code>bedToBigBed</code> utility to create the bigPsl output file (<em>Step 5</em>, above): <pre><code>bedToBigBed -as=bigPsl.as -type=bed12+13 -tab bigPsl.txt hg38.chrom.sizes bigPsl.bb</code></pre></li> <li> Place the newly created bigPsl file (<em>bigPsl.bb</em>) on a web-accessible server (<em>Step 6</em>, above).</li> <li> Construct a track line that points to the bigPsl file (<em>Step 7</em>, above).</li> <li> Create the custom track on the human assembly hg38 (Dec. 2013), and view it in the Genome Browser (<em>Step 8, above</em>).</li> </ol> <h2>Sharing your data with others</h2> <p> If you would like to share your bigPsl 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 bigPsl format</h2> <p> Because bigPsl 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" -->