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/FAQ/FAQgenes.html src/hg/htdocs/FAQ/FAQgenes.html index 3f24f5624b0..a4cfe540110 100755 --- src/hg/htdocs/FAQ/FAQgenes.html +++ src/hg/htdocs/FAQ/FAQgenes.html @@ -202,31 +202,31 @@ <a name="wrong"></a> <h6>I think this transcript looks strange, what shall I do?</h6> <p>The Genome Browser Group only displays transcripts provided by others. But both RefSeq and Gencode have dedicated staff that look manually at each and every transcript and they know everything there is to know about gene models. They are happy to answer your questions and they can change the transcript annotation. Submit your questions via the <a href="https://www.ncbi.nlm.nih.gov/projects/RefSeq/update.cgi" target=_blank>RefSeq contact form</a> or the <a href="https://www.gencodegenes.org/pages/contact.html" target=_blank>Gencode contact form.</a> </p> <a name="duplicates"></a> <h6>Why does the UCSC RefSeq track ("refGene") include duplicates, and some transcripts map to two loci?</h6> -<p>This is related to the question <a href="#ncbiRefSeq">What is the difference between "NCBI RefSeq" and "UCSC RefSeq"?</a> +<p>This is related to the question <a href="#ncbiRefseq">What is the difference between "NCBI RefSeq" and "UCSC RefSeq"?</a> below. Briefly, the UCSC refGene track aligns the RefSeq transcripts to the genome with BLAT, with no special filtering but a 95% identity, the NCBI RefSeq track is NCBI's mapping and the NCBI alignments were filtered using manual annotations to make sure that a transcript is mapped only once, even if it is perfectly aligning twice (there is one exception, genes in the PAR regions, see the paragraph below). NCBI uses manual curation to decide on the best placement, for example, if a gene is annotated on chr4, any alignments, even 100% identical, from other chromosomes are removed. As a result, the UCSC RefSeq track contains duplicates if the transcripts align very well to both loci and alerts the user to this fact, where as the NCBI alignments were filtered manually to make sure that every transcript maps only once. </p> <p> NCBI's transcript mapping, which we provide in our NCBI RefSeq track, does contain a few duplicates, but these have a biological explanation: they are transcripts in the <a target=_blank href='https://en.wikipedia.org/wiki/Pseudoautosomal_region'>pseudoautosomal regions</a>