e5759993329b6e609e9ab825991a90283e714088 mspeir Wed Sep 9 11:17:57 2026 -0700 Help pages: fix broken internal links and restore anchors people still cite, refs #38062 Three groups of anchor problems on the help and FAQ pages. Broken internal links, five pages: posters.html listed a 2022 section that does not exist (no 2022 posters), api.html listed REST and JSON separately after the two sections were merged, docker.html pointed at a #UsrAcct section that is not on that page, FAQgenes.html had a capitalized #ncbiRefSeq where the anchor is #ncbiRefseq, and the genomes.txt settings rows in trackDbHub.v3.html carried no anchors so its own "genome" link missed. Retired anchors that are still cited in twenty years of answers on the genome list. Content moved to its own page and the old anchor was deleted rather than left behind, so the citations land at the top of the page. Reattached seven numeric FAQformat anchors to the Topics entry linking to each format's page. BED, PSL, GFF and GTF were removed from the custom track page in 2012 and never added back to its list of supported formats; added them with the old anchors, which fixes customTrack.html and hgTracksHelp.html together since both include customTrackText.html. Also restored #lines there, and #Session on hgTrackHubHelp.html and #link4 on FAQlink.html. Section anchors on six pages that had none, so a support answer can link to one part of them: bam.html, hic.html, bedgraph.html, ftp.html, net.html and trackDbIndexBb.html. Skipped quickLiftChain.html, oligoMatch.html and cutters.html, which are track description fragments included into the details page rather than standalone pages. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/htdocs/goldenPath/help/bam.html src/hg/htdocs/goldenPath/help/bam.html index ce027327c77..0b08268167d 100755 --- src/hg/htdocs/goldenPath/help/bam.html +++ src/hg/htdocs/goldenPath/help/bam.html @@ -68,30 +68,31 @@ <li> Construct a <a href="hgTracksHelp.html#CustomTracks">custom track</a> using a single <a href="hgTracksHelp.html#TRACK">track line</a>. The most basic version of the "track" line will look something like this: <pre><code> track type=bam name="My BAM" bigDataUrl=<em>http://myorg.edu/mylab/my.sorted.bam</em></code></pre> Again, in addition to <em>http://myorg.edu/mylab/my.sorted.bam</em>, the associated index file <em>http://myorg.edu/mylab/my.sorted.bam.bai</em> must also be available at the same location. If not, you can specify the URL with the <code>bigDataIndex=<em>http://myorg.edu/mylab/my.sorted.bam.bai</em></code></li> <li> Paste the custom track line into the text box in the <a href="../../cgi-bin/hgCustom" target="_blank">custom track management page</a>, click submit and view in the Genome Browser.</li> </ol> +<a id="parameters"></a> <h3>Parameters for BAM custom track definition lines</h3> <p> All options are placed in a single line separated by spaces. In the example below, the lines are broken only for readability. If you copy/paste this example, you must remove the line breaks. Click <a href="examples/bamExample.txt">here</a> for a text version that you can paste without editing.</p> <pre><code> <strong>track type=bam bigDataUrl=</strong><em>http://...</em> <strong>pairEndsByName=</strong><em>.</em> <strong>pairSearchRange=</strong><em>N</em> <strong>bamColorMode=</strong><em>strand|gray|tag|off</em> <strong>bamGrayMode=</strong><em>aliQual|baseQual|unpaired</em> <strong>bamColorTag=</strong><em>XX</em> <strong>minAliQual=</strong><em>N</em> <strong>showNames=</strong><em>on|off</em> <strong>name=</strong><em>track_label</em> @@ -134,30 +135,31 @@ the BAM track configuration page options corresponding to <code>pairEndsByName</code>, <code>minAliQual</code>, <code>bamColorMode</code>, <code>bamGrayMode</code> and <code>bamColorTag</code> in more detail.</p> <p> <code>pairSearchRange</code> applies only when <code>pairEndsByName</code> is given. It allows for a tradeoff of display speed vs. completeness of pairing the paired-end alignments. When paired ends are split or separated by large gaps or introns, but one is viewing a small genomic region, it is necessary to search a large number of bases upstream and downstream of the viewed region in order to find mates of the alignments in the viewed region. However, searching a very large region can be slow, especially when the alignments have deep coverage of the genome. To ensure that all properly paired mates will be found, <code>pairSearchRange</code> should be set to the largest genomic size of a mapped pair. However, it can be set to a smaller size if necessary to speed up the display, at the cost of some items being displayed as unpaired when the mate is too far outside the viewed window.</p> +<a id="example1"></a> <h3>Example #1</h3> <p> In this example, you will create a custom track for an indexed BAM file that is already on a public server — alignments of sequence generated by the <a href="http://1000genomes.org/" target="_blank">1000 Genomes Project</a>.</p> <p> You can paste the URL <code>http://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam</code> directly into the <a href="../../cgi-bin/hgCustom" target="_blank">custom track management page</a> for the human assembly hg18 (May 2006), then press the <em>submit</em> button. On the following page, press the <em>chr21</em> link in the custom track and navigate to position chr21:33,038,946-33,039,092 to see the reads in the new BAM track.</p> <p> Alternatively, you can specify more visualization options by creating a "track" line. The line breaks inserted here for readability must be removed before submitting the track line:</p> <pre><code> track type=bam name="BAM Example One" description="Bam Ex. 1: 1000 Genomes read alignments (individual NA12878)" @@ -166,41 +168,43 @@ bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam</code></pre> <p> Include the following "browser" line to view a small region of chromosome 21 with alignments from the .bam file:</p> <pre><code> browser position chr21:33,038,946-33,039,092</code></pre> <p> Note if you copy/paste the above example, you must remove the line breaks (or, click <a href="examples/bamExampleOne.txt">here</a> for a text version that you can paste without editing).</p> <p> Paste the "browser" line and "track" line into the <a href="../../cgi-bin/hgCustom" target="_blank">custom track management page</a> for the human assembly hg18 (May 2006), then press the "submit" button. On the following page, press the <em>chr21</em> link in the custom track listing to view the BAM track in the Genome Browser.</p> +<a id="example2"></a> <h3>Example #2</h3> <p> In this example, you will create indexed BAM from an existing SAM file. First, save this SAM file <a href="examples/samExample.sam" target="_blank">samExample.sam</a> to your machine. Perform steps 1 and 3-7 in the workflow described above, but substituting <code>samExample.sam</code> for <code>my.sam</code>. On the <a href="../../cgi-bin/hgCustom" target="_blank">custom track management page</a>, click the "add custom tracks" button if necessary and make sure that the genome is set to Human and the assembly is set to Mar. 2006 (hg18) before pasting the track line and submitting. This track line is a little nicer than the one shown in step 6, but remember to remove the line breaks that have been added to the track line for readability (or, click <a href="examples/bamExampleTwo.txt">here</a> for a text version that you can paste without editing):</p> <pre><code> track type=bam name="BAM Example Two" bigDataUrl=<em>http://myorg.edu/mylab/my.sorted.bam</em> description="Bam Ex. 2: Simulated RNA-seq read alignments" visibility=squish db=hg18 chromosomes=chr21 browser position chr21:33,037,317-33,038,137 browser pack mrna</code></pre> +<a id="sharing"></a> <h3>Sharing Your Data with Others</h3> <p> If you would like to share your BAM data track with a colleague, learn how to create a sharable URL by looking at <a href="customTrack.html#SHARE">this page</a>.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->