# crispresso

> Run CRISPResso2 analysis for CRISPR genome editing experiments using Docker. Use this skill when analyzing CRISPR editing outcomes, quantifying indels, evaluating HDR efficiency, or processing base/prime editing data from amplicon sequencing.

- Author: alex90thu
- Repository: alex90thu/skills
- Version: 20260124100437
- Stars: 0
- Forks: 0
- Last Updated: 2026-02-06
- Source: https://github.com/alex90thu/skills
- Web: https://mule.run/skillshub/@@alex90thu/skills~crispresso:20260124100437

---

---
name: crispresso
description: Run CRISPResso2 analysis for CRISPR genome editing experiments using Docker. Use this skill when analyzing CRISPR editing outcomes, quantifying indels, evaluating HDR efficiency, or processing base/prime editing data from amplicon sequencing.
---

# CRISPResso2 Docker Analysis

## Overview

CRISPResso2 is the gold standard tool for analyzing CRISPR genome editing outcomes from amplicon sequencing data. This skill provides Docker-based workflows for running CRISPResso2 analysis without local installation.

## Quick Start

### Prerequisites

- Docker installed and running
- At least 4GB memory allocated to Docker
- FASTQ files from amplicon sequencing

### Basic Analysis Command

```bash
docker run -v ${PWD}:/DATA -w /DATA -i pinellolab/crispresso2 CRISPResso \
  -r1 sample.fastq.gz \
  -a AATGTCCCCCAATGGGAAGTTCATCTGGCACTGCCCACAGGTGAGGAGGTCATGATCCCCTTCTGGAGCTCCCAACGGGCCGTGGTCTGGTTCATCATCTGTAAGAATGGCTTCAAGAGGCTCGGCTGTGGTT
```

### Required Parameters

| Parameter | Description |
|-----------|-------------|
| `-r1, --fastq_r1` | First FASTQ file (required) |
| `-a, --amplicon_seq` | Reference amplicon sequence |

### Common Optional Parameters

| Parameter | Default | Description |
|-----------|---------|-------------|
| `-r2, --fastq_r2` | - | Second FASTQ for paired-end |
| `-g, --guide_seq` | - | sgRNA sequence (without PAM) |
| `-n, --name` | auto | Output name |
| `-o, --output_folder` | `.` | Output directory |

## Workflow Decision Tree

```
What type of analysis do you need?
|
+-- Single sample analysis --> Use CRISPResso (this guide)
|
+-- Multiple samples --> Use CRISPRessoBatch
|   See: references/batch-analysis.md
|
+-- Pooled amplicons --> Use CRISPRessoPooled
|   See: references/pooled-analysis.md
|
+-- Whole genome --> Use CRISPRessoWGS
|   See: references/wgs-analysis.md
|
+-- Compare two samples --> Use CRISPRessoCompare
    See: references/compare-analysis.md
```

## Common Use Cases

### 1. Basic Indel Analysis

Analyze editing outcomes with default settings:

```bash
docker run -v '${PWD}:/DATA' -w /DATA -i pinellolab/crispresso2 CRISPResso \
  -r1 reads.fastq.gz \
  -a AMPLICON_SEQUENCE \
  -g GUIDE_SEQUENCE_20NT
```

### 2. Paired-End Reads

```bash
docker run -v '${PWD}:/DATA' -w /DATA -i pinellolab/crispresso2 CRISPResso \
  -r1 reads_R1.fastq.gz \
  -r2 reads_R2.fastq.gz \
  -a AMPLICON_SEQUENCE \
  -g GUIDE_SEQUENCE
```

### 3. HDR Analysis

Analyze homology-directed repair with expected sequence:

```bash
docker run -v '${PWD}:/DATA' -w /DATA -i pinellolab/crispresso2 CRISPResso \
  -r1 reads.fastq.gz \
  -a WILDTYPE_AMPLICON \
  -e EXPECTED_HDR_AMPLICON \
  -g GUIDE_SEQUENCE
```

### 4. Base Editor Analysis

For C>T or A>G base editing experiments:

```bash
docker run -v '${PWD}:/DATA' -w /DATA -i pinellolab/crispresso2 CRISPResso \
  -r1 reads.fastq.gz \
  -a AMPLICON_SEQUENCE \
  -g GUIDE_SEQUENCE \
  --base_editor_output \
  --conversion_nuc_from C \
  --conversion_nuc_to T
```

### 5. Prime Editing Analysis

```bash
docker run -v' ${PWD}:/DATA' -w /DATA -i pinellolab/crispresso2 CRISPResso \
  -r1 reads.fastq.gz \
  -a AMPLICON_SEQUENCE \
  --prime_editing_pegRNA_spacer_seq SPACER_SEQUENCE \
  --prime_editing_pegRNA_extension_seq EXTENSION_SEQUENCE \
  --prime_editing_nicking_guide_seq NICK_GUIDE_SEQUENCE
```

## Output Files

CRISPResso2 generates a comprehensive output folder containing:

| File | Description |
|------|-------------|
| `CRISPResso_quantification_of_editing_frequency.txt` | Main editing statistics |
| `Alleles_frequency_table.zip` | All observed allele frequencies |
| `CRISPResso_mapping_statistics.txt` | Read alignment stats |
| `CRISPResso2_report.html` | Interactive HTML report |
| `*.png` | Visualization plots |

## Quality Control Parameters

```bash
# Filter by average read quality (Phred33)
--min_average_read_quality 30

# Filter by single base quality
--min_single_bp_quality 20

# Convert low quality bases to N
--min_bp_quality_or_N 20
```

## Quantification Window

Control where modifications are counted:

```bash
# Window size (bp from cleavage site)
-w 1                    # Default: 1bp each side

# Window center (relative to sgRNA 3' end)
-wc -3                  # Default: -3 (typical Cas9 cut)

# Custom coordinates
-qwc 50-60              # Explicit bp range
```

## Performance Options

```bash
# Use multiple CPU cores
-p 4                    # Or use 'max' for all cores

# Skip regenerating existing results
--no_rerun

# Reduce output verbosity
-v 1                    # 1-4, default 3
```

## Advanced Usage

For detailed parameter documentation, see:

- [references/parameters.md](references/parameters.md) - Complete parameter reference
- [references/batch-analysis.md](references/batch-analysis.md) - Batch processing guide
- [references/prime-editing.md](references/prime-editing.md) - Prime editing specifics
- [references/base-editing.md](references/base-editing.md) - Base editing analysis

## Helper Scripts

This skill includes helper scripts for common workflows:

```bash
# Run analysis with common defaults
python scripts/run_crispresso.py -r1 reads.fq.gz -a AMPLICON -g GUIDE

# Batch process multiple samples
python scripts/batch_runner.py --sample_sheet samples.csv
```

## Troubleshooting

### Docker Permission Issues

On Linux/Mac, you may need to run with sudo or add your user to the docker group.

### Memory Errors

Increase Docker memory allocation in Docker Desktop settings (recommend 4GB+).

### Alignment Failures

- Check amplicon sequence orientation matches your reads
- Try lowering `--default_min_aln_score` (default 60)
- Verify guide sequence doesn't include PAM

### No Reads Aligned

- Verify amplicon sequence is correct
- Check FASTQ quality with FastQC
- Try `--auto` to infer amplicon from reads