This track is distributed via the DANIO-CODE project's hub, but was produced by the Shawn Burgess laboratory at NHGRI: a genome-wide catalogue of predicted CRISPR/Cas9 target sites, in three sets (all sites, and those beginning with GG or GA, the dinucleotides efficiently transcribed by the guide-RNA polymerases). It is placed here rather than under gene models, next to where the browser keeps its own CRISPR guide tracks on other genomes.
The target sites are drawn as blocks, in the colors stored in the data files. All three tracks are off by default.
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 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.
For automated download and analysis, the annotations are stored in bigBed files that can be downloaded from our download server. The files are danRer11_sp6cas_N18_20.colored.bb (all target sites), danRer11_sp6cas_GGN16_18NGG.colored.bb (GG targets) and danRer11_sp6cas_GAN16_18NGG.colored.bb (GA targets). 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/danRer11_sp6cas_N18_20.colored.bb \
-chrom=chr1 -start=20000000 -end=20100000 stdout
The original data files 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.