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) 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 @@

Construct a custom track using a single track line. The most basic version of the "track" line will look something like this:

    track type=bam name="My BAM" bigDataUrl=http://myorg.edu/mylab/my.sorted.bam

Again, in addition to http://myorg.edu/mylab/my.sorted.bam, the associated index file http://myorg.edu/mylab/my.sorted.bam.bai must also be available at the same location. If not, you can specify the URL with the bigDataIndex=http://myorg.edu/mylab/my.sorted.bam.bai

Paste the custom track line into the text box in the custom track management page, click submit and view in the Genome Browser.

Parameters for BAM custom track definition lines

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 here for a text version that you can paste without editing.

    track type=bam bigDataUrl=http://...
         pairEndsByName=. 
         pairSearchRange=N
         bamColorMode=strand|gray|tag|off 
         bamGrayMode=aliQual|baseQual|unpaired
         bamColorTag=XX 
         minAliQual=N 
         showNames=on|off
         name=track_label 
@@ -134,30 +135,31 @@
 the BAM track configuration page options corresponding to pairEndsByName,
 minAliQual, bamColorMode, bamGrayMode and
 bamColorTag in more detail.
 
 pairSearchRange applies only when pairEndsByName 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, pairSearchRange 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.
 
+
 Example #1
 
 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 1000 Genomes Project.
 
 You can paste the URL http://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam
 directly into the custom track management page
 for the human assembly hg18 (May 2006), then press the submit button. On the following 
 page, press the chr21 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.
 
 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:
     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
 
 Include the following "browser" line to view a small region of chromosome 21 with 
 alignments from the .bam file: 
         browser position chr21:33,038,946-33,039,092
 
 Note if you copy/paste the above example, you must remove the line breaks (or, click 
 here for a text version that you can paste without 
 editing).
 
 Paste the "browser" line and "track" line into the 
 custom track management page for the human 
 assembly hg18 (May 2006), then press the "submit" button. On the following page, press 
 the chr21 link in the custom track listing to view the BAM track in the Genome Browser.
 
+
 Example #2
 
 In this example, you will create indexed BAM from an existing SAM file. First, save this SAM file 
 samExample.sam to your machine. Perform steps 
 1 and 3-7 in the workflow described above, but substituting samExample.sam for 
 my.sam. On the custom track management 
 page, 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 
 here for a text version that you can paste without 
 editing):
     track type=bam name="BAM Example Two"
         bigDataUrl=http://myorg.edu/mylab/my.sorted.bam
         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
 
+
 Sharing Your Data with Others
 
 If you would like to share your BAM data track with a colleague, learn how to create a sharable 
 URL by looking at this page.