Documentation

Start a screen

Use Plan to choose a study level and calculate cell, DNA, PCR, and sequencing requirements. The tutorial follows both supported workflows from planning through Review.

Gene-level screening supports CRISPR-KO, CRISPRi, and CRISPRa. Variant-level screening supports human GRCh38 SNVs with the Prime Editing MAVE workflow; its current analysis measures pegRNA abundance, not editing efficiency.

Try sample data

Use the Load example and Download example actions beside the relevant inputs in Build, QC, and Analyze. Example files pass through the same input and result workflows as uploaded files.

For an example output, load the sample FASTQ and manifest in Library QC, then inspect read assignment, missing reagents, abundance inequality, and target coverage. In Analyze, load the T0 and endpoint example to inspect replicate QC and ranked effects. Demonstration data test software behavior; they are not independent biological validation.

Interpret results

PLAN estimates infection with a Poisson model. At MOI 0.3, about 85.7% of infected cells are expected to have one integration. It tracks cell, DNA-template, and sequencing-read coverage separately; more reads cannot recover templates lost before PCR.

Representation

Planned or observed cells, molecules, or reads per reagent. These are distinct units; a high read count cannot restore lost independent DNA templates.

Library QC

Read assignment and detected/missing reagents describe the amplified plasmid pool. Gini and count CV describe abundance unevenness, not biological effect.

Screen analysis

Compare the stated T0 and endpoint samples with appropriate biological replicates. Ranked gene or variant results are abundance-based and depend on the uploaded manifest and contrast.

Prime Editing

PRIDICT2 ranks design candidates; its score is not measured editing efficiency. The current MAVE result does not measure endogenous or sensor editing.

See the Glossary for terminology and References for external sources.