bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/bigNarrowPeak.html src/hg/htdocs/goldenPath/help/bigNarrowPeak.html index fbb7cb0fe71..13bc6bcdae0 100755 --- src/hg/htdocs/goldenPath/help/bigNarrowPeak.html +++ src/hg/htdocs/goldenPath/help/bigNarrowPeak.html @@ -70,42 +70,42 @@ <p> <strong>Step 1.</strong> Create a bigNarrowPeak file. The first six fields of the bigNarrowPeak bed6+4 format are described by the basic BED file format shown <a href="../../FAQ/FAQformat.html#format1">here</a>. You can also read about narrowPeak (or point-source peak), the precursor to bigNarrowPeak, <a href="../../FAQ/FAQformat.html#format12">here</a>. Your bigNarrowPeak file must also contain the four extra fields described in the autoSql file definition shown above: <code>signalValue, pValue, qValue, peak</code>. Your bigNarrowPeak file must be sorted first on the <code>chrom</code> field, and secondarily on the <code>chromStart</code> field. You can use the UNIX <code>sort</code> command to do this:</p> <pre><code>sort -k1,1 -k2,2n unsorted.bed > input.bed</code></pre> <p> <strong>Step 2.</strong> Download the <code>bedToBigBed</code> program 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> Create the bigNarrowPeak file from your sorted input file using the <code>bedToBigBed</code> utility:</p> <pre><code><strong>bedToBigBed</strong> -as=bigNarrowPeak.as -type=bed6+4 bigNarrowPeak.txt chrom.sizes myBigNarrowPeak.bb</code></pre> <p> <strong>Step 5.</strong> Move the newly created bigNarrowPeak file (<em>myBigNarrowPeak.bb</em>) to a web-accessible http, https, or ftp location.</p> <p> <strong>Step 6.</strong> Construct a <a href="hgTracksHelp.html#CustomTracks">custom track</a> using a single <a href="hgTracksHelp.html#TRACK">track line</a>. Note that any of the track attributes listed <a href="customTrack.html#TRACK">here</a> are applicable to tracks of type bigNarrowPeak. The basic version of the track line will look something like this:</p> @@ -148,31 +148,31 @@ <p> After this example bigNarrowPeak track is loaded in the Genome Browser, click on a peak in the browser's track display to view the details page for that peak.</p> <a name="example2"></a> <h3>Example #2</h3> <p> In this example, you will create your own bigNarrowPeak file from an existing bigNarrowPeak input file.</p> <ol> <li> Save the example bed6+4 input file, <em><a href="examples/bigNarrowPeak.txt">bigNarrowPeak.txt</a></em>, to your computer (<em>Step 1</em> in <em>Creating a bigNarrowPeak track</em>, above).</li> <li> - Download the <a href="http://hgdownload.soe.ucsc.edu/admin/exe/"><code>bedToBigBed</code></a> + Download the <a href="http://hgdownload.gi.ucsc.edu/admin/exe/"><code>bedToBigBed</code></a> utility (<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/bigNarrowPeak.as"><em>bigNarrowPeak.as</em></a> to your computer.</li> <li> Run the <code>bedToBigBed</code> utility to create the bigNarrowPeak output file (<em>step 4</em>, above): <pre><code><B>bedToBigBed</B> -type=bed6+4 -tab -as=bigNarrowPeak.as bigNarrowPeak.txt hg38.chrom.sizes bigNarrowPeak.bb</code></pre></li> <li> Place the newly created bigNarrowPeak file (<em>bigNarrowPeak.bb</em>) on a web-accessible server (<em>Step 5</em>, above).</li> <li> @@ -223,45 +223,45 @@ longLabel bigNarrowPeak Example bigDataUrl http://genome.ucsc.edu/goldenPath/help/examples/bigNarrowPeak.bb</pre></code> </p> <h2>Sharing your data with others</h2> <p> If you would like to share your bigNarrowPeak 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> and the additional <a href="customTrack.html#optParams">URL optional parameters</a> section.</p> <h2>Extracting data from bigBed format</h2> <p> Because the bigNarrowPeak 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> Such tools can be used to obtain only features within a given range, for example: <p><tt> -bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/danRer10/transMap/V4/danRer10.refseq.transMapV4.bigPsl +bigBedToBed http://hgdownload.gi.ucsc.edu/gbdb/danRer10/transMap/V4/danRer10.refseq.transMapV4.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout </tt> </> <p> As with all UCSC Genome Browser programs, 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 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) before running the <code>bedToBigBed</code> program. </p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->