bio-crispr-screens-base-editing-analysis

CRISPResso2 for Base Editing

Goal: Quantify base editing efficiency and bystander edits from amplicon sequencing.

Approach: Run CRISPResso with --base_editor_output and the expected edited amplicon sequence to measure target base conversion, bystander edits, and indel frequencies.

## Key Metrics

| Metric | Description |
|--------|-------------|
| Editing efficiency | % reads with target base change |
| Bystander edits | Unintended edits in editing window |
| Indel frequency | Insertions/deletions (should be low) |
| Purity | Target edit without bystanders |

## C->T conversion (or G->A on opposite strand)

CRISPResso --fastq_r1 reads.fq.gz \
    --amplicon_seq $AMPLICON \
    --guide_seq $GUIDE \
    --base_editor_output \
    --conversion_nuc_from C \
    --conversion_nuc_to T