Library QC
Inspect either variant-level pegRNA or gene-level sgRNA plasmid-library representation before screening.
QC modality
Variant-level Prime Editing MAVE QC assigns reads to full-identity pegRNAs and variants; spacer-only assignment is not accepted. Gene-level CRISPR QC assigns reads to sgRNAs and genes.
Prime Editing library QC
QC needs both the sequenced plasmid library and the designed library information. Upload a plasmid FASTQ/FASTQ.GZ plus the pegRNA manifest exported by Build (or an equivalent table describing every ordered pegRNA). The manifest defines the intended library; it is required to identify missing pegRNAs and variant coverage. Reads are assigned by complete insert identity, not spacer alone.
Upload plasmid-library QC inputs
QC needs both the sequenced plasmid library and the designed library information. Upload a FASTQ/FASTQ.GZ plus the CSV or TSV manifest for the library you ordered or cloned. The manifest must list every intended guide with guide identifier, gene, and spacer sequence; it is required to quantify missing guides and gene-level completeness. Files are processed only for this request.
Reference QC reports
Load these compact comparison reports when inspecting the QC thresholds and failure modes.
Metrics
- Mapping rate
- The fraction of sequenced reads assigned unambiguously to a spacer in the supplied manifest. Low values can indicate a read-orientation, trimming, library, or sequencing issue.
- Guide detection
- The number and percentage of manifest guides with at least one mapped read. It measures whether the designed library is present at all.
- Missing-guide fraction
- The percentage of designed guides with zero mapped reads. A high value means representation was lost before or during sequencing.
- Gini coefficient
- Unevenness of guide counts: 0 means perfectly even; larger values mean a small set of guides dominates. Lower is better for a pooled library.
- Count coefficient of variation
- Standard deviation divided by mean guide count. It complements Gini by showing relative spread in abundance.
- Low-count fraction
- The percentage of guides below the QC low-count threshold. These guides are vulnerable to dropout in cell culture and downstream comparisons.
- Gene-level completeness
- The fraction of targeted genes retaining at least one detected guide. This reveals whether dropout is concentrated in biologically important targets.