3f640d70bab0bc124024a977d8836756318c1852 gperez2 Fri Sep 4 14:39:51 2026 -0700 Fixing malformed HTML in three track description pages caught by hgTablesTest: encode4LongRnaTranscripts.html had a stray html/body wrapper, and knownGeneVM33.html/knownGeneVM36.html each had an extra closing </ul>. No RM. diff --git src/hg/makeDb/trackDb/human/hg38/encode4LongRnaTranscripts.html src/hg/makeDb/trackDb/human/hg38/encode4LongRnaTranscripts.html index a57057f5dcf..a9de3d4bc8b 100644 --- src/hg/makeDb/trackDb/human/hg38/encode4LongRnaTranscripts.html +++ src/hg/makeDb/trackDb/human/hg38/encode4LongRnaTranscripts.html @@ -1,92 +1,86 @@ -<!DOCTYPE html> -<html> -<head> -</head> - -<body> <h2>Description</h2> <p> The ENCODE4 long-read RNA-seq collection annotates trancripts using numerical triplets representing the identity of the start site, exon junction chain, and transcript end site of each transcript. This method reveals how promoter selection, splice pattern, and 3’ processing are deployed across human tissues. </p> <h2>Display Conventions</h2> <p> Transcript names include a triplet annotation that represents transcript start site, exon junction chain, and transcript end site. For example, if transcript A has the label [1,2,3] and transcript B is labeled [1,1,3], then those transcripts share start and end sites but have a different combination of exons. Here is an exmaple drawn from hg38 at the INSIG1 locus:</p> <img src="../images/encode4LongReadTranscriptsHelp.png"> <p> In this example, the first two transcripts marked by arrows have the same start site ("1") and the same set of exons ("8"), but they have different end sites ("2" vs "1"). Similarly, the second two marked transcripts have the same start site ("1"), but a different set of exons ("8" vs "9") and a different end site ("1" vs "2"). </p> <p> GENCODE V29 and V40 were used as reference data; any transcript not present in either of these is colored <font color=0000FF>blue</font>.</p> <p> Mouseover on transcripts shows their ENCODE gene ID and the tissue or cell line where it’s most highly expressed and its TPM in that sample. </p> <h2>Data Access</h2> The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For automated analysis, the data may be queried from our <a href="../../goldenPath/help/api.html">REST API</a>.</p> <p> The data underlying this track is available in the file <a href="https://hgdownload.gi.ucsc.edu/gbdb/$db/encode4/encode4LongRnaTranscripts.bb">encode4LongRna.bb</a>. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>, which is available on our <a href="http://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads">download server</a>. For example, to extract only annotations in a given region, you could use the following command: </p> <pre> bigBedToBed -chrom=chr1 -start=100000 -end=100500 https://hgdownload.gi.ucsc.edu/gbdb/$db/encode4LongRna.bb stdout </pre> <p> Please refer to our <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">mailing list archives</a> for questions, or our <a href="../../FAQ/FAQdownloads.html#downloads36">Data Access FAQ</a> for more information. </p> <h2>Methods</h2> <p> Data were retrieved from <a href="https://zenodo.org/records/15116042">https://zenodo.org/records/15116042</a>. The <tt>human_ucsc_transcripts.gtf</tt> was converted to BED format, and expression and CDS data added from the relevant files using a custom script. </p> <h2>Credits</h2> <p> Thanks to Fairlie Reese for providing data access and for helpful feedback. </p> <h2>References</h2> <p> Reese F, Williams B, Balderrama-Gutierrez G, Wyman D, Çelik MH, Rebboah E, Rezaie N, Trout D, Razavi-Mohseni M, Jiang Y <em>et al</em>. <a href="https://doi.org/10.1101/2023.05.15.540865" target="_blank"> The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity</a>. <em>bioRxiv</em>. 2023 May 16;. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/37292896" target="_blank">37292896</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10245583/" target="_blank">PMC10245583</a> </p>