f5c96c14557e69252db6935d20ea55bdd250e519 max Fri Sep 4 17:12:57 2026 -0700 DANIO-CODE as native danRer11 tracks, alpha only. Converts the DANIO-CODE consortium's public track hub for danRer11 into a native trackDb: 897 stanzas under one superTrack, with 11 containers for RNA-seq, CAGE-seq, ChIP-seq, 3P-seq, Hi-C, regulatory elements, cell types, COPEs/DOPEs, validated enhancers, conservation and consensus promoters. The 879 data files, 69 GB, are mirrored under /gbdb/danRer11/danioCode and are byte-identical to the consortium's copies. Four cell-type subtracks are left out because their files 404 on the consortium's server. refs #38265 diff --git src/hg/makeDb/trackDb/zebrafish/danRer11/dcComparativeGenomics.html src/hg/makeDb/trackDb/zebrafish/danRer11/dcComparativeGenomics.html new file mode 100644 index 00000000000..02a22ce3979 --- /dev/null +++ src/hg/makeDb/trackDb/zebrafish/danRer11/dcComparativeGenomics.html @@ -0,0 +1,97 @@ +<h2>Description</h2> + +<p> +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>