343fea87263b7c29116af560510356a194e4da0b lrnassar Tue Oct 29 12:51:15 2019 -0700 Sprucing up the crisprAll html, and removing a hardcoded hg19 mention refs#24296 diff --git src/hg/makeDb/trackDb/crisprAll.html src/hg/makeDb/trackDb/crisprAll.html index 95c38a9..154f5e0 100644 --- src/hg/makeDb/trackDb/crisprAll.html +++ src/hg/makeDb/trackDb/crisprAll.html @@ -107,52 +107,60 @@ datasets, the correlation of the prediction with other assays was around 25% lower, see <a href="#References">Haeussler et al. 2016</a>. At the time of writing, there is no independent dataset available yet to determine the Moreno-Mateos accuracy for each score percentile range.</p> <h3>Track methods</h3> <p> The entire $organism ($db) genome was scanned for the -NGG motif. Flanking 20mer guide sequences were aligned to the genome with BWA and scored with MIT Specificity scores using the command-line version of crispor.org. Non-unique guide sequences were skipped. 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 +2014 algorithms, among others.</p> +<p> +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> 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="../cgi-bin/hgTables?db=${db}&hgta_track=crisprAllTargets&hgta_regionType=range">Table Browser</a>. +For small programmatic positional queries, the track can be accessed using our +<a href="/goldenPath/help/api.html">REST API</a>. For genome-wide data or +automated analysis, CRISPR genome annotations can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/$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 +as a bigBedFile.</p> +<p> +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 +can also be used to obtain only features within a given range, e.g.</p> +<p> +<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> <p> Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J <em>et al</em>.