---
name: mkurman/deeptools
source: https://app.decimal.ai/s/mkurman-deeptools@1/SKILL.md
source_sha256: 65a8fc7f3764
---

----|----------|------|-------|
| Human | GRCh38/hg38 | 2,913,022,398 | `--effectiveGenomeSize 2913022398` |
| Mouse | GRCm38/mm10 | 2,652,783,500 | `--effectiveGenomeSize 2652783500` |
| Zebrafish | GRCz11 | 1,368,780,147 | `--effectiveGenomeSize 1368780147` |
| *Drosophila* | dm6 | 142,573,017 | `--effectiveGenomeSize 142573017` |
| *C. elegans* | ce10/ce11 | 100,286,401 | `--effectiveGenomeSize 100286401` |

Complete table with read-length-specific values: `references/effective_genome_sizes.md`

## Common Parameters Across Tools

Many deepTools commands share these options:

**Performance:**
- `--numberOfProcessors, -p`: Enable parallel processing (always use available cores)
- `--region`: Process specific regions for testing (e.g., `chr1:1-1000000`)

**Read Filtering:**
- `--ignoreDuplicates`: Remove PCR duplicates (recommended for most analyses)
- `--minMappingQuality`: Filter by alignment quality (e.g., `--minMappingQuality 10`)
- `--minFragmentLength` / `--maxFragmentLength`: Fragment length bounds
- `--samFlagInclude` / `--samFlagExclude`: SAM flag filtering

**Read Processing:**
- `--extendReads`: Extend to fragment length (ChIP-seq: YES, RNA-seq: NO)
- `--centerReads`: Center at fragment midpoint for sharper signals

## Best Practices

### File Validation
**Always validate files first** using `scripts/validate_files.py` to check:
- File existence and readability
- BAM indices present (.bai files)
- BED format correctness
- File sizes reasonable

### Analysis Strategy

1. **Start with QC**: Run correlation, coverage, and fingerprint analysis before proceeding
2. **Test on small regions**: Use `--region chr1:1-10000000` for parameter testing
3. **Document commands**: Save full command lines for reproducibility
4. **Use consistent normalization**: Apply same method across samples in comparisons
5. **Verify genome assembly**: Ensure BAM and BED files use matching genome builds

### ChIP-seq Specific

- **Always extend reads** for ChIP-seq: `--extendReads 200`
- **Remove duplicates**: Use `--ignoreDuplicates` in most cases
- **Check enrichment first**: Run plotFingerprint before detailed analysis
- **GC correction**: Only apply if significant bias detected; never use `--ignoreDuplicates` after GC correction

### RNA-seq Specific

- **Never extend reads** for RNA-seq (would span splice junctions)
- **Strand-specific**: Use `--filterRNAstrand forward/reverse` for stranded libraries
- **Normalization**: CPM for bins, RPKM for genes

### ATAC-seq Specific

- **Apply Tn5 correction**: Use alignmentSieve with `--ATACshift`
- **Fragment filtering**: Set appropriate min/max fragment lengths
- **Check nucleosome pattern**: Fragment size plot should show ladder pattern

### Performance Optimization

1. **Use multiple processors**: `--numberOfProcessors 8` (or available cores)
2. **Increase bin size** for faster processing and smaller files
3. **Process chromosomes separately** for memory-limited systems
4. **Pre-filter BAM files** using alignmentSieve to create reusable filtered files
5. **Use bigWig over bedGraph**: Compressed and faster to process

## Troubleshooting

### Common Issues

**BAM index missing:**
```bash
samtools index input.bam
```

**Out of memory:**
Process chromosomes individually using `--region`:
```bash
bamCoverage --bam input.bam -o chr1.bw --region chr1
```

**Slow processing:**
Increase `--numberOfProcessors` and/or increase `--binSize`

**bigWig files too large:**
Increase bin size: `--binSize 50` or larger

### Validation Errors

Run validation script to identify issues:
```bash
python scripts/validate_files.py --bam *.bam --bed regions.bed
```

Common errors and solutions explained in script output.

## Reference Documentation

This skill includes comprehensive reference documentation:

### references/tools_reference.md
Complete documentation of all deepTools commands organized by category:
- BAM and bigWig processing tools (9 tools)
- Quality control tools (6 tools)
- Visualization tools (3 tools)
- Miscellaneous tools (2 tools)

Each tool includes:
- Purpose and overview
- Key parameters with explanations
- Usage examples
- Important notes and best practices

**Use this reference when:** Users ask about specific tools, parameters, or detailed usage.

### references/workflows.md
Complete workflow examples for common analyses:
- ChIP-seq quality control workflow
- ChIP-seq complete analysis workflow
- RNA-seq coverage workflow
- ATAC-seq analysis workflow
- Multi-sample comparison workflow
- Peak region analysis workflow
- Troubleshooting and performance tips

**Use this reference when:** Users need complete analysis pipelines or workflow examples.

### references/normalization_methods.md
Comprehensive guide to normalization methods:
- Detailed explanation of each method (RPGC, CPM, RPKM, BPM, etc.)
- When to use each method
- Formulas and interpretation
- Selection guide by experiment type
- Common pitfalls and solutions
- Quick reference table

**Use this reference when:** Users ask about normalization, comparing samples, or which method to use.

### references/effective_genome_sizes.md
Effective genome size values and usage:
- Common organism values (human, mouse, fly, worm, zebrafish)
- Read-length-specific values
- Calculation methods
- When and how to use in commands
- Custom genome calculation instructions

**Use this reference when:** Users need genome size for RPGC normalization or GC bias correction.

## Helper Scripts

### scripts/validate_files.py

Validates BAM, bigWig, and BED files for deepTools analysis. Checks file existence, indices, and format.

**Usage:**
```bash
python scripts/validate_files.py --bam sample1.bam sample2.bam \
    --bed peaks.bed --bigwig signal.bw
```

**When to use:** Before starting any analysis, or when troubleshooting errors.

### scripts/workflow_generator.py

Generates customizable bash script templates for common deepTools workflows.

**Available workflows:**
- `chipseq_qc`: ChIP-seq quality control
- `chipseq_analysis`: Complete ChIP-seq analysis
- `rnaseq_coverage`: Strand-specific RNA-seq coverage
- `atacseq`: ATAC-seq with Tn5 correction

**Usage:**
```bash
# List workflows
python scripts/workflow_generator.py --list

# Generate workflow
python scripts/workflow_generator.py chipseq_qc -o qc.sh \
    --input-bam Input.bam --chip-bams "ChIP1.bam ChIP2.bam" \
    --genome-size 2913022398 --threads 8

# Run generated workflow
chmod +x qc.sh
./qc.sh
```

**When to use:** Users request standard workflows or need template scripts to customize.

## Assets

### assets/quick_reference.md

Quick reference card with most common commands, effective genome sizes, and typical workflow pattern.

**When to use:** Users need quick command examples without detailed documentation.

## Handling User Requests

### For New Users

1. Start with installation verification
2. Validate input files using `scripts/validate_files.py`
3. Recommend appropriate workflow based on experiment type
4. Generate workflow template using `scripts/workflow_generator.py`
5. Guide through customization and execution

### For Experienced Users

1. Provide specific tool commands for requested operations
2. Reference appropriate sections in `references/tools_reference.md`
3. Suggest optimizations and best practices
4. Offer troubleshooting for issues

### For Specific Tasks

**"Convert BAM to bigWig":**
- Use bamCoverage with appropriate normalization
- Recommend RPGC or CPM based on use case
- Provide effective genome size for organism
- Suggest relevant parameters (extendReads, ignoreDuplicates, binSize)

**"Check ChIP quality":**
- Run full QC workflow or use plotFingerprint specifically
- Explain interpretation of results
- Suggest follow-up actions based on results

**"Create heatmap":**
- Guide through two-step process: computeMatrix → plotHeatmap
- Help choose appropriate matrix mode (reference-point vs scale-regions)
- Suggest visualization parameters and clustering options

**"Compare samples":**
- Recommend bamCompare for two-sample comparison
- Suggest multiBamSummary + plotCorrelation for multiple samples
- Guide normalization method selection

### Referencing Documentation

When users need detailed information:
- **Tool details**: Direct to specific sections in `references/tools_reference.md`
- **Workflows**: Use `references/workflows.md` for complete analysis pipelines
- **Normalization**: Consult `references/normalization_methods.md` for method selection
- **Genome sizes**: Reference `references/effective_genome_sizes.md`

Search references using grep patterns:
```bash
# Find tool documentation
grep -A 20 "^### toolname" references/tools_reference.md

# Find workflow
grep -A 50 "^## Workflow Name" references/workflows.md

# Find normalization method
grep -A 15 "^### Method Name" references/normalization_methods.md
```

## Example Interactions

**User: "I need to analyze my ChIP-seq data"**

Response approach:
1. Ask about files available (BAM files, peaks, genes)
2. Validate files using validation script
3. Generate chipseq_analysis workflow template
4. Customize for their specific files and organism
5. Explain each step as script runs

**User: "Which normalization should I use?"**

Response approach:
1. Ask about experiment type (ChIP-seq, RNA-seq, etc.)
2. Ask about comparison goal (within-sample or between-sample)
3. Consult `references/normalization_methods.md` selection guide
4. Recommend appropriate method with justification
5. Provide command example with parameters

**User: "Create a heatmap around TSS"**

Response approach:
1. Verify bigWig and gene BED files available
2. Use computeMatrix with reference-point mode at TSS
3. Generate plotHeatmap with appropriate visualization parameters
4. Suggest clustering if dataset is large
5. Offer profile plot as complement

## Key Reminders

- **File validation first**: Always validate input files before analysis
- **Normalization matters**: Choose appropriate method for comparison type
- **Extend reads carefully**: YES for ChIP-seq, NO for RNA-seq
- **Use all cores**: Set `--numberOfProcessors` to available cores
- **Test on regions**: Use `--region` for parameter testing
- **Check QC first**: Run quality control before detailed analysis
- **Document everything**: Save commands for reproducibility
- **Reference documentation**: Use comprehensive references for detailed guidance