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/dcComparativeGenomics.html src/hg/makeDb/trackDb/zebrafish/danRer11/dcComparativeGenomics.html index 02a22ce3979..63224f61730 100644 --- src/hg/makeDb/trackDb/zebrafish/danRer11/dcComparativeGenomics.html +++ src/hg/makeDb/trackDb/zebrafish/danRer11/dcComparativeGenomics.html @@ -1,97 +1,94 @@ <h2>Description</h2> <p> +This track is part of the <a href="hgTrackUi?g=danioCode">DANIO-CODE</a> track collection. Regulatory elements often leave no mark in the genome sequence itself, but they do tend to change more slowly over evolutionary time than the DNA around them. Comparing a genome with those of related species therefore highlights the parts that are under selection, and stretches outside genes that stay conserved are good candidates for regulatory function. These are usually called conserved non-coding elements. </p> <p> This track holds conservation and CRISPR resources for danRer11 produced by the Shawn Burgess laboratory at NHGRI, which the DANIO-CODE consortium includes in its track hub. It has two parts. The conservation part is a phastCons score computed from an alignment of zebrafish with grass carp, common carp and goldfish, together with the conserved non-coding elements called from that score. The CRISPR part is a genome-wide catalogue of predicted CRISPR/Cas9 target sites, in three sets: all target sites, those beginning with GG, and those beginning with GA. The GG and GA sets matter in practice because those dinucleotides are efficiently transcribed by the polymerases used to make the guide RNA. </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> The phastCons track is a graph, auto-scaled to the window. The conserved non-coding elements and the CRISPR target sites are drawn as blocks, in the colors stored in the data files. All five tracks are off by default. </p> <h2>Methods</h2> <p> The phastCons scores were computed from a whole-genome alignment of zebrafish with three other cyprinid fishes, grass carp, common carp and goldfish, and conserved non-coding elements were called from the scores. CRISPR/Cas9 target sites were predicted genome-wide for the SP6-transcribed guide format, once without a constraint on the first two bases and once each for guides starting with GG and with GA. These data were produced by the Shawn Burgess laboratory at NHGRI and are distributed from <a href="https://research.nhgri.nih.gov/manuscripts/Burgess/zebrafish/" target="_blank"> their own site</a>, which is also where questions about them are best directed. </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>dcComparativeGenomics</i>. </p> <p> For automated download and analysis, the annotations are stored in bigWig and bigBed files that can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/" target="_blank">our download server</a>. The files are <tt>ZF_GC_CC_GF.danRer11.bw</tt> (phastCons), <tt>ZF_GC_CC_GF.danRer11.bb</tt> (conserved non-coding elements) and <tt>danRer11_sp6cas_N18_20.colored.bb</tt>, <tt>danRer11_sp6cas_GGN16_18NGG.colored.bb</tt> and <tt>danRer11_sp6cas_GAN16_18NGG.colored.bb</tt> (CRISPR targets). 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/ZF_GC_CC_GF.danRer11.bb \ -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 Shawn Burgess laboratory at NHGRI for producing and distributing these data, and to the DANIO-CODE consortium for including them in their track hub. </p>