8c2f7318d8d821de9b2a25750586a94ab5e8c1bb lrnassar Fri Nov 15 18:50:19 2024 -0800 Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM. diff --git src/hg/makeDb/trackDb/crisprAll.html src/hg/makeDb/trackDb/crisprAll.html index 71d9ae6..594649a 100644 --- src/hg/makeDb/trackDb/crisprAll.html +++ src/hg/makeDb/trackDb/crisprAll.html @@ -1,24 +1,24 @@ <h2>Description</h2> <p> This track shows the DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme from <em>S. pyogenes</em> (PAM: NGG) over the entire $organism ($db) genome. CRISPR target sites were annotated with predicted specificity (off-target effects) and predicted efficiency (on-target cleavage) by various -algorithms through the tool <a href="http://crispor.tefor.net/" +algorithms through the tool <a href="http://crispor.gi.ucsc.edu/" target="_blank">CRISPOR</a>. Sp-Cas9 usually cuts double-stranded DNA three or four base pairs 5' of the PAM site. </p> <h2>Display Conventions and Configuration</h2> <p> The track "CRISPR Targets" shows all potential -NGG target sites across the genome. The target sequence of the guide is shown with a thick (exon) bar. The PAM motif match (NGG) is shown with a thinner bar. Guides are colored to reflect both predicted specificity and efficiency. Specificity reflects the "uniqueness" of a 20mer sequence in the genome; the less unique a sequence is, the more likely it is to cleave other locations of the genome (off-target effects). Efficiency is the frequency of cleavage at the target site (on-target efficiency).</p> @@ -106,41 +106,41 @@ their own training data. Especially for the Moreno-Mateos score, the results are too optimistic, due to overfitting. When evaluated on independent 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/" target="_blank">Crispor downloads page</a>, which +href="http://crispor.gi.ucsc.edu/downloads/" target="_blank">Crispor downloads page</a>, which includes the Doench 2016, Moreno-Mateos 2015 and Bae 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. <a href="http://crispor.tefor.net/" target="_blank">Crispor.org</a> can display both +the new scores. <a href="http://crispor.gi.ucsc.edu/" target="_blank">Crispor.org</a> 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=${db}&hgta_track=crisprAllTargets&hgta_regionType=range">Table Browser</a> or the <a href="/cgi-bin/hgIntegrator?db=${db}">Data Integrator</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.</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