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Frequently asked questions

Our Scientific Applications Support team has assembled a list of frequently asked questions to help you find answers quickly. Filter using one or more categories to focus on specific topics, or use the search bar to perform a text search.

How sensitive is the rhAmpSeq™ CRISPR Analysis System?

With CRISPAltRations™, the software behind the rhAmpSeq CRISPR Analysis Tool, we analyzed the editing in three experimental replicates of 20 paired, treated, and control Cas9-edited loci. The treated samples had known indel editing levels (0.05, 0.10, 0.20, 0.50, 1.0, 2.0, and 3.4%), while the control samples had noise signals ranging from 0–0.4%.

Using the Fisher’s Exact Test (with a threshold of p<0.5), we show that 95% sensitivity and specificity were obtained for detecting indels down to 0.5%. This analysis assumed that there were:

  • more than 5000 paired-end reads in both the treatment and control samples
  • ·normal levels of background indel noise (<0.4% indels)
  • treatment sample loci with editing >0.5%
  • libraries prepared with the rhAmpSeq CRISPR Library Kit and sequencing data analyzed by the rhAmpSeq CRISPR Analysis Tool (powered by CRISPAltRations®).


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