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/crispr.html src/hg/makeDb/trackDb/crispr.html index bee42ee..851c6fc 100644 --- src/hg/makeDb/trackDb/crispr.html +++ src/hg/makeDb/trackDb/crispr.html @@ -1,24 +1,24 @@ <h2>Description</h2> <p> This track shows regions of the genome within 200 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 200 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 200 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. </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> and are located in the <a href="http://hgdownload.soe.ucsc.edu/gbdb/${db}/crispr/">/gbdb/${db}/crispr</a> directory of our downloads server. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>, 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 <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool