gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/deeptools/references/effective_genome_sizes.md

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 uniquely mapped (may consider edit distance)

Common Organism Values

Using Non-N Bases Method

Organism	Assembly	Effective Size	Full Command
Human	GRCh38/hg38	2,913,022,398	--effectiveGenomeSize 2913022398
Human	GRCh37/hg19	2,864,785,220	--effectiveGenomeSize 2864785220
Mouse	GRCm39/mm39	2,654,621,837	--effectiveGenomeSize 2654621837
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	WBcel235/ce11	100,286,401	--effectiveGenomeSize 100286401
C. elegans	ce10	100,258,171	--effectiveGenomeSize 100258171

Human (GRCh38) by Read Length

For quality-filtered reads, values vary by read length:

Read Length	Effective Size
50bp	~2.7 billion
75bp	~2.8 billion
100bp	~2.8 billion
150bp	~2.9 billion
250bp	~2.9 billion

Mouse (GRCm38) by Read Length

Read Length	Effective Size
50bp	~2.3 billion
75bp	~2.5 billion
100bp	~2.6 billion

Usage in deepTools

The effective genome size is most commonly used with:

bamCoverage with RPGC normalization

bamCoverage --bam input.bam --outFileName output.bw \
    --normalizeUsing RPGC \
    --effectiveGenomeSize 2913022398

bamCompare with RPGC normalization

bamCompare -b1 treatment.bam -b2 control.bam \
    --outFileName comparison.bw \
    --scaleFactorsMethod RPGC \
    --effectiveGenomeSize 2913022398

computeGCBias / correctGCBias

computeGCBias --bamfile input.bam \
    --effectiveGenomeSize 2913022398 \
    --genome genome.2bit \
    --fragmentLength 200 \
    --biasPlot bias.png

Choosing the Right Value

For most analyses: Use the non-N bases method value for your reference genome

For filtered data: If you apply strict quality filters or remove multimapping reads, consider using the read-length-specific values

When unsure: Use the conservative non-N bases value - it's more widely applicable

Common Shortcuts

deepTools also accepts these shorthand values in some contexts:

• hs or GRCh38: 2913022398
• mm or GRCm38: 2652783500
• dm or dm6: 142573017
• ce or ce10: 100286401

Check your specific deepTools version documentation for supported shortcuts.

Calculating Custom Values

For custom genomes or assemblies, calculate the non-N bases count:

# Using faCount (UCSC tools)
faCount genome.fa | grep "total" | awk '{print $2-$7}'

# Using seqtk
seqtk comp genome.fa | awk '{x+=$2}END{print x}'

References

For the most up-to-date effective genome sizes and detailed calculation methods, see:

• deepTools documentation: https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
• ENCODE documentation for reference genome details