2e1806a6ac3094a2653e9276dd60746cabec0484 dschmelt Wed Jul 10 17:11:50 2019 -0700 Adding note about positional data only #23803 diff --git src/hg/makeDb/trackDb/crisprAll.html src/hg/makeDb/trackDb/crisprAll.html index c4f5eb8..95c38a9 100644 --- src/hg/makeDb/trackDb/crisprAll.html +++ src/hg/makeDb/trackDb/crisprAll.html @@ -118,36 +118,37 @@ Flanking sequences were extracted from the genome and input for Crispor efficiency scoring, available from the <a href="http://crispor.tefor.net/downloads/">Crispor downloads page</a>, which includes the Doench 2016, Moreno-Mateos 2015 and Bae 2014 algorithms, among others. Note that the Doench 2016 scores were updated by the Broad institute in 2017 ("Azimuth" update). As a result, earlier versions of the track show the old Doench 2016 scores and this version of the track shows new Doench 2016 scores. Old and new scores are almost identical, they are correlated to 0.99 and for more than 80% of the guides the difference is below 0.02. However, for very few guides, the difference can be bigger. In case of doubt, we recommend the new scores. Crispor.org can display both scores and many more with the "Show all scores" link.</p> <H2>Data Access</H2> <p> -The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>. -For automated analysis, the genome annotation is stored in a bigBed file that -can be downloaded from -<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/${track}/" target="_blank">our download server</a>. -The files for this track are called <tt>crispr.bb</tt> and <tt>crisprDetails.tab</tt>. Individual -regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>, +Positional data can be explored interactively with the +<a href="../cgi-bin/hgTables?db=hg19&hgta_track=crisprAllTargets&hgta_regionType=range">Table Browser</a>. +For genome-wide data or automated analysis, CRISPR genome annotations can be downloaded from +<a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/crisprAll/" target="_blank">our download server</a> +as a bigBedFile. The files for this track are called <tt>crispr.bb</tt>, which lists positions and +scores, and <tt>crisprDetails.tab</tt>, which has information about off-target matches. Individual +regions or whole genome annotations can be obtained using our tool <tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a pre-compiled binary for your system. Instructions for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain only features within a given range, e.g. <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/${db}/${track}/crispr.bb -chrom=chr21 -start=0 -end=1000000 stdout</tt> </p> <h2>Credits</h2> <p> Track created by Maximilian Haeussler, with helpful input from Jean-Paul Concordet (MNHN Paris) and Alberto Stolfi (NYU). </p> <a name="References"></a> <h2>References</h2>