bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/bedMethyl.html src/hg/htdocs/goldenPath/help/bedMethyl.html index 35624070b35..5906707d80c 100755 --- src/hg/htdocs/goldenPath/help/bedMethyl.html +++ src/hg/htdocs/goldenPath/help/bedMethyl.html @@ -1,178 +1,178 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser bedMethyl Track Format" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>bedMethyl and bigMethyl Track Format</h1> <p> The <a target="_blank" href="https://www.encodeproject.org/data-standards/wgbs/">bedMethyl</a> format is an extension of the standard <a href="/FAQ/FAQformat.html#format1">BED 9 format</a> used to display DNA methylation site data in a genome browser. This format is useful for base-resolution methylation data generated by bisulfite sequencing or direct methylation detection methods such as long-read sequencing. By including both methylation level and support (coverage), bedMethyl provides a detailed view of methylation across the genome.</p> <p>The bedMethyl format includes the information of a <b>BED 9</b> along with additional fields:</p> <ul> <li>Valid Coverage: Reads with valid modification call <li>Percent Modified: Percent of valid calls that are modified <li>Modified calls: Number of calls with a modified base <li>Canonical calls: Number of calls with a canonical base <li>Other modification calls: Number of calls with a modified base, other modifications <li>Reads with a deletion: Number of reads with a deletion at this reference position <li>Low-confidence calls: Number of calls where the probability of the call was below the threshold <li>Reads with a base mismatch: Number of reads with a base other than the canonical base for this modification <li>Reads with no modification call: Number of reads aligned to this reference position, with the correct canonical base, but without a base modification call </ul> <p class="text-center"> <img "1080" height="148" src="../../images/bedMethylEx.jpg"> </p> <p>The items are colored from <b><font color="#0000FF">0%</font></b> methylated modified (blue) to <b><font color="#FF0000">100%</font></b> (red). Hovering over an item or clicking it shows the additional details found in bedMethyl. Methylation calls are shown separately for CpG sites (<b>m</b>) and non-CpG (CHG/CHH) sites (<b>h</b>).</p> <a name=bedMethyl></a> <h2>Creating a bedMethyl custom track</h2> <a name="example1"></a> <h3>Example #1</h3> <p> In this example, you will create a bedMethyl custom track using bedMethyl data for the hg38 assembly.</p> <ol> <li>Paste the following track line into the <a href="../../cgi-bin/hgCustom?db=hg19">custom track management page</a> for the human assembly hg38. <pre><code> track type=bedMethyl name="bedmethyl example" description="bedMethyl custom track" visibility="pack" chr21 5010053 5010054 h 0 + 5010053 5010054 255,0,0 1 0.00 0 0 1 0 0 0 0 chr21 5010053 5010054 m 0 + 5010053 5010054 255,0,0 1 0.00 1 0 0 0 0 0 0 chr21 5010215 5010216 h 0 + 5010215 5010216 255,0,0 1 30.00 0 0 1 0 0 0 0 chr21 5010215 5010216 m 0 + 5010215 5010216 255,0,0 1 30.00 1 0 0 0 0 0 0 chr21 5010331 5010332 h 0 + 5010331 5010332 255,0,0 1 70.00 0 0 1 0 0 0 0 chr21 5010331 5010332 m 0 + 5010331 5010332 255,0,0 1 70.00 1 0 0 0 0 0 0 chr21 5010335 5010336 h 0 + 5010335 5010336 255,0,0 1 100.00 0 0 1 0 0 0 0 chr21 5010335 5010336 m 0 + 5010335 5010336 255,0,0 1 100.00 1 0 0 0 0 0 0 </code></pre></li> <li>Click the "submit" button.</li> <li>Go to chr21:5,010,030-5,010,408 to see the data.</li> </ol> </p> <a name=bigMethyl></a> <h2>bigMethyl Format</h2> <p>The <b>bigMethyl</b> format is the indexed version of bedMethyl using bedToBigBed. See <a href="bigBed.html">bigBed format</a>. The bigMethyl format is more efficient to display in the Genome Browser, and it offers more trackDb options, which will allow for customization. The following autoSql definition is an example on how to specify bigMethyl files. This definition, contained in the file <a href="examples/bigMethyl.as"><em>bigMethyl.as</em></a>, is pulled in when the <code>bedToBigBed</code> utility is run with the <code>-as=bigMethyl.as</code> option.</p> <pre><code> table bigMethyl "bigMethyl bedMethyl" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chrom" uint chromEnd; "End position in chrom" string name; "dbSNP Reference SNP (rs) identifier or :" uint score; "Score from 0-1000, derived from p-value" char[1] strand; "Unused. Always '.'" uint thickStart; "Start position in chrom" uint thickEnd; "End position in chrom" uint color; "Red (positive effect) or blue (negative). Brightness reflects pvalue" string nValidCov; "Valid Coverage" double percMod; "Percent Modified" uint nMod; "Number of calls with a modified base" uint nCanon; "Number of calls with a canonical base" uint nOther; "Number of calls with a modified base, other modification" uint nDelete; "Number of reads with a deletion at this reference position" uint nFail; "Number of calls where the probability of the call was below the threshold" uint nDiff; "Number of reads with a base other than the canonical base for this modification" uint nNoCall; "Number of reads aligned to this reference position, with the correct canonical base, but without a base modification call" ) </code></pre> <p>The first 9 fields of this bigMethyl format are the same as the first 9 fields of the standard BED format.</p> <h2>Creating a bigMethyl custom track</h2> <a name="example2"></a> <h3>Example #2</h3> <p> In this example, you will create a bigMethyl file to display as a custom track.</p> <ol> <li> Save <a href="examples/bedMethyl.bed">this bedMethyl file</a> to your computer.</li> <li> Save the autoSql files <a href="examples/bigMethyl.as"><em>bigMethyl.as</em></a> to your computer.</li> <li> Download the <code>bedToBigBed</code> - <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">utility</a>.</li> + <a href="http://hgdownload.gi.ucsc.edu/admin/exe/">utility</a>.</li> <li> Use the <code>bedToBigBed</code> utility to create a bigMethyl file from your sorted bedMethyl file, using the <em>bedMethyl.bed</em> file and <em>chrom.sizes</em> files created above. </p> <pre><code><strong>bedToBigBed</strong> -as=bigMethyl.as -type=bed9+9 bedMethyl.bed https://genome.ucsc.edu/goldenPath/help/hg38.chrom.sizes bigMethyl.bb</code></pre></li> <p> <li> Move the newly created bigMethyl file (<em>bigMethyl.bb</em>) to a web-accessible http, https, or ftp location. At this point you should have a URL to your data, such as "https://institution.edu/bigMethyl.bb", and the file should be accessible outside of your institution/hosting providers network. For more information on where to host your data, please see the <a href="hgTrackHubHelp.html#Hosting">Hosting</a> section of the Track Hub Help documentation. Construct a custom track line with a bigDataUrl parameter pointing to the newly created bigMethyl file.</p> <pre><code>track type=bigMethyl name="bigMethyl Example" description="A bigMethyl file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigMethyl.bb visibility=pack</code></pre></li> <li> Go to chr21:5,010,030-5,010,408 to see the data.</li> </ol> <a name=sharing_data></a> <h2>Sharing your data with others</h2> <p> Custom tracks can also be loaded via one URL line. <a href="../../cgi-bin/hgTracks?ignoreCookie=1&db=hg38&position=chr21:5,010,030-5,010,408&hgct_customText=track%20type=bigMethyl%20name=Example%20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigMethyl.bb%20visibility=pack" target="_blank">This link</a> loads the same <em>bigMethyl.bb</em> track and sets additional display parameters from <a href="#example2">Example 2</a> in the URL:</p> <pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?ignoreCookie=1&db=hg38&position=chr21:5,010,030-5,010,408&hgct_customText=track%20type=bigMethyl%20name=Example %20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigMethyl.bb %20visibility=pack</code></pre> <p> If you would like to share your bigMethyl data track with a colleague, you can learn how to create a URL link to your data by looking at <a href="customTrack.html#EXAMPLE6">Example #6</a> on the custom track help page.</p> <a name=extracting_data></a> <h2>Extracting data from the bigMethyl format</h2> <p> Because the bigMethyl 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> <a name=troubleshooting></a> <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" -->