The executive summary generated at the end of the Cas 9 data analysis workflow using the EPI2ME Labs platform provides the key metrics used to establish whether an experiment has been successful.

One of the metrics is the Target Coverage which is the most important value to focus on. It mostly depends on probe design and input DNA quality and it will be an average value if multiple targets are being assessed in the same experiments.

For a well-designed Cas9 targeted experiment, we would expect >=100x coverage for a single target.

Coverage plots generated by the tutorial show overlapping directional coverage for the region of interest to assess performance from both ends separately (as shown below).

For multiple targets in the same experiment, while the headline value provides an average coverage, it is helpful to look at individual coverage of the regions.

If the coverage is lower than 100x for a particular region of interest, the corresponding crRNA probe may not be performing well.

This may be improved by including additional probes to either side of the region of interest for redundancy to boost target coverage.

More information can be found in the Targeted, amplification-free DNA sequencing using CRISPR/Cas9 info sheet, the Cas9 targeted sequencing protocol.