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/crispr10K.html src/hg/makeDb/trackDb/crispr10K.html index cb24aa3..e38482c 100644 --- src/hg/makeDb/trackDb/crispr10K.html +++ src/hg/makeDb/trackDb/crispr10K.html @@ -1,24 +1,24 @@ <h2>Description</h2> <p> This track shows regions of the genome within 10,000 bp of transcribed regions and DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme from <em>S. pyogenes</em> (PAM: NGG). 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>. </p> <h2>Display Conventions and Configuration</h2> <p> The track "CRISPR Regions" shows the regions of the genome where target sites were analyzed, i.e. within 10,000 bp of transcribed regions as annotated by Ensembl transcript models.</p> <p> The track "CRISPR Targets" shows the target sites in these regions. 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 @@ -109,31 +109,31 @@ 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> Exons as predicted by Ensembl Gene models were used, extended by 10,000 basepairs on each side, searched 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 +href="http://crispor.gi.ucsc.edu/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 the 10k 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