Base editing vs. Knockout Reports- Which to Pick?

  • Updated

The Tapestri Genome Editing Software allows users to select either a Knockout (KO) or Base Editing (BE) report. The report one chooses should align with the experimental approach one used to generate the genome editing data:

  • Knockout (KO) Report: This report should be selected if one used a gene editor to induce double-stranded breaks at one or more target sites and exploited non-homologous end joining (NHEJ) repair, resulting in insertions/deletions (INDELS) ranging 1-50 bp in length. The KO Report defines “edits” as indels and shows only indels in the automated report. Information on any single-nucleotide variants is available in the h5 file. 
  • Base Editing (BE) Report: This report should be selected if one used a base editor to induce single-nucleotide substitutions at one or more target sites. The report shows SNVs within the on-target activity window for one or multiple on-targets and shows SNVs and indels for predicted off-target edits. The report does not display indel information in the on-target activity window(s), but this information is accessible in the h5 file.

Can I pick both reports?

We highly recommend only selecting the report that aligns with the strategy you used to edit your cells. These reports have been designed to provide appropriate information for each approach while reducing misinterpretation from the occurrence of false positive events. If you have a need for both SNV and indel information, please contact our support team (


Can I analyze Knock-ins/ Homology-Directed Repair using the KO Report?

This version of the Genome Editing Pipeline was designed to analyze only INDELs (ranging from 1-50 bp) and SNVs. It was not designed to distinguish between donor DNA templates and integrated sequences. It is also not recommended to use the pipeline to analyze INDELs > 50 bp in length.


Can I analyze large deletions using the KO Report?

Deletions of length up to 50 bp have been tested using the Genome Editing Pipeline. Therefore we cannot guarantee the accuracy of analyzing larger deletion events.

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