This track is distributed via the DANIO-CODE project's hub, but was produced by the Shawn Burgess laboratory at NHGRI: 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 same laboratory's CRISPR/Cas9 target-site predictions, also distributed through the DANIO-CODE hub, have their own CRISPR/Cas9 Targets track.
The phastCons track is a graph, auto-scaled to the window. The conserved non-coding elements are drawn as blocks, in the colors stored in the data file. Both tracks are off by default.
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. These data were produced by the Shawn Burgess laboratory at NHGRI and are distributed from their own site, which is also where questions about them are best directed.
At UCSC the tracks were converted from the consortium's public track hub at trackhub2.genereg.net/DANIO-CODE with the script danioCodeHubToRa.py, and the data files were copied from the same server. The data themselves were not modified. The steps are documented in our makeDoc.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API, track=dcComparativeGenomics.
For automated download and analysis, the annotations are stored in bigWig and bigBed files that can be downloaded from our download server. The files are ZF_GC_CC_GF.danRer11.bw (phastCons) and ZF_GC_CC_GF.danRer11.bb (conserved non-coding elements). Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, 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 here. The tool can also be used to obtain features within a given range, for example
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/ZF_GC_CC_GF.danRer11.bb \
-chrom=chr1 -start=20000000 -end=20100000 stdout
The original data files, and the sample and protocol metadata behind them, are available from the DANIO-CODE data coordination center at danio-code.zfin.org and from the consortium's track hub at trackhub2.genereg.net/DANIO-CODE.
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.