Analyze screen data

Analyze either variant-level Prime Editing MAVE screens or gene-level sgRNA screens with an explicit, non-mixed analysis target.

Analysis modality

Choose the biological level represented by the abundance data. Prime Editing MAVE maps full-identity pegRNA abundance to variants; gene-level CRISPR analysis maps sgRNA abundance to genes. These inputs must not be mixed.

FASTQ counting

Upload one FASTQ/FASTQ.GZ and its guide manifest. CRISPR Screen Guider previews read orientation and guide start before running the pinned MAGeCK counter.

Columns: guide_id, gene, sequence.
Download FASTQ example Download manifest example

T0 versus endpoint FASTQ analysis

Upload the sequencing reads from both timepoints and one shared guide manifest. CRISPR Screen Guider counts each FASTQ with MAGeCK, validates guide identity, then compares T0 with endpoint automatically.

Columns: guide_id, gene, sequence.
Download T0 FASTQ example Download endpoint FASTQ example

Count-table analysis

Primary gene-level analysis uses MAGeCK. Upload UTF-8 CSV or TSV with sgRNA, Gene, then one column per sample. Sample roles are declared below; they are never inferred from filenames.

One matrix containing both T0 and endpoint columns, or use the two separate matrix uploads below.
CSV or TSV. Required fields: sample_id, condition, timepoint, replicate, sample_type, contrast_group.
Paste standard CSV/TSV here, or upload the file above. The server validates sample roles before analysis.
Download count-table example Download sample-sheet example