3265eee7833f0ce97bf38bb585b7803d79640517 dschmelt Wed Jul 3 13:52:22 2019 -0700 Changing crisprAll track super to normal and adding a few tdb tags #23514 diff --git src/hg/makeDb/trackDb/crisprAll.html src/hg/makeDb/trackDb/crisprAll.html index 9a26a15..e95bd6f 100644 --- src/hg/makeDb/trackDb/crisprAll.html +++ src/hg/makeDb/trackDb/crisprAll.html @@ -1,35 +1,31 @@ <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/" 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.</p> - -<p> -The track "CRISPR Targets" shows the target sites in these regions. +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> <p>Shades of gray stand for sites that are hard to target specifically, as the 20mer is not very unique in the genome:</p> <table class="stdTbl" style="width:100%"> <tr><td style="width:50px; background-color:#969696"></td><td>impossible to target: target site has at least one identical copy in the genome and was not scored</td></tr> <tr><td style="width:50px; background-color:#787878"></td><td>hard to target: many similar sequences in the genome that alignment stopped, repeat?</td></tr> <tr><td style="width:50px; background-color:#505050"></td><td>hard to target: target site was aligned but results in a low specificity score <= 50 (see below)</td></tr> </table>