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skills/deeptools/references/effective_genome_sizes.md

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+# 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
+```bash
+bamCoverage --bam input.bam --outFileName output.bw \
+    --normalizeUsing RPGC \
+    --effectiveGenomeSize 2913022398
+```
+
+### bamCompare with RPGC normalization
+```bash
+bamCompare -b1 treatment.bam -b2 control.bam \
+    --outFileName comparison.bw \
+    --scaleFactorsMethod RPGC \
+    --effectiveGenomeSize 2913022398
+```
+
+### computeGCBias / correctGCBias
+```bash
+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:
+
+```bash
+# 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