17710ebe183000560daf8e3cfb56a86eaa382f58 mspeir Mon May 19 09:48:53 2025 -0700 making tweaks to ENCODE long read transcripts track desc + config, refs #31368 diff --git src/hg/makeDb/trackDb/human/hg38/encode4.html src/hg/makeDb/trackDb/human/hg38/encode4.html index 62d78a37c99..cd27a45c7e5 100644 --- src/hg/makeDb/trackDb/human/hg38/encode4.html +++ src/hg/makeDb/trackDb/human/hg38/encode4.html @@ -5,57 +5,74 @@ <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. -<br> +of exons.</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>. -<br> +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. +expressed and its TPM in that sample. </p> <h2>Data Access</h2> The raw data can be explored interactively with the -<a href="https://genome.ucsc.edu/cgi-bin/hgTables">Table Browser</a> or the -<a href="https://genome.ucsc.edu/cgi-bin/hgIntegrator">Data Integrator</a>. +<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="https://genome.ucsc.edu/goldenPath/help/api.html">REST API</a>.<br> +<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="https://genome.ucsc.edu/FAQ/FAQdownloads.html#downloads36">Data Access FAQ</a> +<a href="../../FAQ/FAQdownloads.html#downloads36">Data Access FAQ</a> for more information. </p> <h2>Methods</h2> <p> -Data were retrieved from https://zenodo.org/records/15116042. The transcript gtf -was converted to Bed format, and expression and CDS data added from the relevant files using a -custom script. +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;.