76eabae1c28bb07c02af6a12fa9222c348b039d9 max Sun Sep 6 07:02:29 2026 -0700 DANIO-CODE: open each subtrack description with the sentence saying that the track is part of the DANIO-CODE container, linking to its hgTrackUi page, instead of burying it in a paragraph at the end of the description. refs #38265 diff --git src/hg/makeDb/trackDb/zebrafish/danRer11/dcConsensus_promoters.html src/hg/makeDb/trackDb/zebrafish/danRer11/dcConsensus_promoters.html index 2ead03d6796..4045c4788b8 100644 --- src/hg/makeDb/trackDb/zebrafish/danRer11/dcConsensus_promoters.html +++ src/hg/makeDb/trackDb/zebrafish/danRer11/dcConsensus_promoters.html @@ -1,114 +1,111 @@ <h2>Description</h2> <p> +This track is part of the <a href="hgTrackUi?g=danioCode">DANIO-CODE</a> track collection. A promoter is the region at which transcription of a gene begins. In vertebrates a promoter rarely uses a single start base; it fires from a cluster of neighboring positions, and which position dominates can change between developmental stages. CAGE sequences the first bases of capped RNAs and therefore measures these start positions directly. </p> <p> This track shows 28,142 consensus promoters, called by combining the CAGE tag clusters of all DANIO-CODE samples into one set that is not tied to a single stage. It is intended as a stage-independent reference set of promoter positions. The per-sample tag clusters that go into it are in the <a href="hgTrackUi?g=dcCAGEseqComposite">DC CAGE-seq</a> track. </p> -<p> -This track is part of the <a href="hgTrackUi?g=danioCode">DANIO-CODE</a> collection. -</p> - <h2>Display Conventions and Configuration</h2> <p> Promoters are drawn as blocks. The score reflects the CAGE expression supporting the promoter. </p> <h2>Methods</h2> <p> The DANIO-CODE consortium assembled 1,802 zebrafish developmental genomics datasets, 1,438 of them already published and 366 generated by consortium members, and reprocessed all of them from the raw sequencing reads so that samples from different laboratories and different protocols can be compared with each other. ChIP-seq and ATAC-seq were run through the ENCODE pipelines, CAGE-seq through the FANTOM pipeline, and Hi-C and 4C-seq through the pipelines of the groups that produced them. The pipelines are published at <a href="https://gitlab.com/danio-code" target="_blank">gitlab.com/danio-code</a>, and samples were assigned to developmental stages using ZFIN and ENCODE nomenclature. See Baranasic <em>et al</em>. 2022 for details. </p> <p> CAGE libraries from all developmental stages were processed with the FANTOM pipeline, tag clusters were called per sample, and the clusters were combined across samples into a consensus set. </p> <p> At UCSC the tracks were converted from the consortium's public track hub at <a href="https://trackhub2.genereg.net/DANIO-CODE/DANIO-CODE.hub.txt" target="_blank"> trackhub2.genereg.net/DANIO-CODE</a> with the script <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/danioCode" target="_blank">danioCodeHubToRa.py</a>, and the data files were copied from the same server. The data themselves were not modified. The steps are documented in <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/danRer11/danioCode.txt" target="_blank">our makeDoc</a>. </p> <h2>Data Access</h2> <p> The data can be explored interactively in table format with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a> and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our <a href="https://api.genome.ucsc.edu">API</a>, track=<i>dcConsensus_promoters</i>. </p> <p> For automated download and analysis, the annotations are stored in bigBed files that can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/" target="_blank">our download server</a>. The file is <tt>consens.canonical.danRer11.bigBed</tt>. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain features within a given range, for example </p> <pre>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/consens.canonical.danRer11.bigBed \ -chrom=chr1 -start=20000000 -end=20100000 stdout</pre> <p> The original data files, and the sample and protocol metadata behind them, are available from the DANIO-CODE data coordination center at <a href="https://danio-code.zfin.org" target="_blank">danio-code.zfin.org</a> and from the consortium's track hub at <a href="https://trackhub2.genereg.net/DANIO-CODE/DANIO-CODE.hub.txt" target="_blank"> trackhub2.genereg.net/DANIO-CODE</a>. </p> <h2>Credits</h2> <p> Thanks to the DANIO-CODE consortium for collecting, reprocessing and publishing these data, and to the laboratories that produced the original datasets. </p> <h2>References</h2> <p> Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/35789323" target="_blank"> Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis- regulatory elements</a>. <em>Nat Genet</em>. 2022 Jul;54(7):1037-1050. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35789323" target="_blank">35789323</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9279159/" target="_blank">PMC9279159</a> </p>