b788a707887a79434941ee37b1c5f5c496995c70 kuhn Thu Jan 20 07:14:25 2022 -0800 added definition of CFD score diff --git src/hg/makeDb/trackDb/crisprAll.html src/hg/makeDb/trackDb/crisprAll.html index 154f5e0..7db918b 100644 --- src/hg/makeDb/trackDb/crisprAll.html +++ src/hg/makeDb/trackDb/crisprAll.html @@ -55,31 +55,32 @@ also shown in parentheses after the percentile.</li> <li>The <a href="https://www.crisprscan.org/">Moreno-Mateos 2015 Efficiency score</a> should be used instead of the Doench 2016 score when transcribing the guide in vitro with a T7 promoter, e.g. for injections in mouse, zebrafish or Xenopus embryos. The Moreno-Mateos score is given in percentiles and the raw value in parentheses, see the note above.</li> </ol> </p> <p>Click onto features to show all scores and predicted off-targets with up to four mismatches. The Out-of-Frame score by <a href="#References">Bae et al. 2014</a> is correlated with the probability that mutations induced by the guide RNA will disrupt the open reading frame. The authors recommend out-of-frame scores > 66 to create knock-outs with a single guide efficiently.<p> -<p>Off-target sites are sorted by the CFD score (<a href="https://www.nature.com/articles/nbt.3437" +<p>Off-target sites are sorted by the CFD (Cutting Frequency Determination) +score (<a href="https://www.nature.com/articles/nbt.3437" target="_blank">Doench et al. 2016</a>). The higher the CFD score, the more likely there is off-target cleavage at that site. Off-targets with a CFD score < 0.023 are not shown on this page, but are available when following the link to the external CRISPOR tool. When compared against experimentally validated off-targets by <a href="#References">Haeussler et al. 2016</a>, the large majority of predicted off-targets with CFD scores < 0.023 were false-positives. For storage and performance reasons, on the level of individual off-targets, only CFD scores are available.</p> <h2>Methods</h2> <h3>Relationship between predictions and experimental data</h3> <p> Like most algorithms, the MIT specificity score is not always a perfect