effective_genome_sizes

Effective genome size refers to the length of the "mappable" genome - regions that can be uniquely mapped by sequencing reads. This metric is crucial for proper normalization in many deepTools commands.

Skills
Scientific
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Install (Claude Code)

mkdir -p .claude/skills/effective-genome-sizes && curl -fsSL https://doutorai.pt/data/lib/skills__effective-genome-sizes.md -o .claude/skills/effective-genome-sizes/SKILL.md

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Content

# Effective Genome Sizes

## Definition

Effective genome size refers to the length of the "mappable" genome - regions that can be uniquely mapped by sequencing reads. This metric is crucial for proper normalization in many deepTools commands.

## Why It Matters

- Required for RPGC normalization (`--normalizeUsing RPGC`)
- Affects accuracy of coverage calculations
- Must match your data processing approach (filtered vs unfiltered reads)

## Calculation Methods

1. **Non-N bases**: Count of non-N nucleotides in genome sequence
2. **Unique mappability**: Regions of specific size that can be uni

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