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/dcRNAseqComposite.html src/hg/makeDb/trackDb/zebrafish/danRer11/dcRNAseqComposite.html index 8745c579795..686b803dc53 100644 --- src/hg/makeDb/trackDb/zebrafish/danRer11/dcRNAseqComposite.html +++ src/hg/makeDb/trackDb/zebrafish/danRer11/dcRNAseqComposite.html @@ -1,119 +1,116 @@ <h2>Description</h2> <p> -This track shows RNA-seq read coverage for 361 zebrafish samples collected by the -DANIO-CODE consortium, covering 31 developmental stages from the 1-cell stage through +This track is part of the <a href="hgTrackUi?g=danioCode">DANIO-CODE</a> track collection. +It shows RNA-seq read coverage for 361 zebrafish samples collected by the +consortium, covering 31 developmental stages from the 1-cell stage through epiboly, somitogenesis and organogenesis to the adult fish. The consortium used 139 of these samples to build an improved transcript annotation containing 31,458 genes and 55,596 transcripts, among them 726 long non-coding RNA genes and 167 transcripts of uncertain coding potential that Ensembl had not annotated. </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> Every sample is shown as a coverage graph. For strand-specific libraries there are two graphs per sample: coverage on the forward strand in red and coverage on the reverse strand in blue. Unstranded libraries have a single graph. </p> <p> Nothing is displayed until samples are selected on the track configuration page. There are more than 500 individual graphs, so turn on only the ones you need; the display becomes very slow otherwise. Samples can be filtered by developmental stage, by sequencing sample accession and by strand. Each graph is auto-scaled to the data in the window, so the height of a peak can be compared within one sample but not between samples. </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> The RNA-seq samples come from 18 laboratories, including the Schier, Giraldez, Busch-Nentwich, Sauka-Spengler, Wardle, Zon, Mathavan, Bartel and Mueller laboratories, and were originally deposited under accessions such as GSE32900, GSE47558, GSE44075, GSE75356 and PRJEB12982. The accession of each sample is shown in its track description line. </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>dcRNAseqComposite</i>. </p> <p> For automated download and analysis, the annotations are stored in bigWig files that can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/" target="_blank">our download server</a>. There is one file per sample and strand, named after the DANIO-CODE sample accession, for example <tt>DCD002238SQ_pos.bigWig</tt>. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigWigToBedGraph</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>bigWigToBedGraph http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/DCD002238SQ_pos.bigWig \ -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>