@synsci/cli-darwin-x64-baseline 1.1.77 → 1.1.78

package/bin/skills/deeptools/references/normalization_methods.md

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+# deepTools Normalization Methods
+
+This document explains the various normalization methods available in deepTools and when to use each one.
+
+## Why Normalize?
+
+Normalization is essential for:
+1. **Comparing samples with different sequencing depths**
+2. **Accounting for library size differences**
+3. **Making coverage values interpretable across experiments**
+4. **Enabling fair comparisons between conditions**
+
+Without normalization, a sample with 100 million reads will appear to have higher coverage than a sample with 50 million reads, even if the true biological signal is identical.
+
+---
+
+## Available Normalization Methods
+
+### 1. RPKM (Reads Per Kilobase per Million mapped reads)
+
+**Formula:** `(Number of reads) / (Length of region in kb × Total mapped reads in millions)`
+
+**When to use:**
+- Comparing different genomic regions within the same sample
+- Adjusting for both sequencing depth AND region length
+- RNA-seq gene expression analysis
+
+**Available in:** `bamCoverage`
+
+**Example:**
+```bash
+bamCoverage --bam input.bam --outFileName output.bw \
+    --normalizeUsing RPKM
+```
+
+**Interpretation:** RPKM of 10 means 10 reads per kilobase of feature per million mapped reads.
+
+**Pros:**
+- Accounts for both region length and library size
+- Widely used and understood in genomics
+
+**Cons:**
+- Not ideal for comparing between samples if total RNA content differs
+- Can be misleading when comparing samples with very different compositions
+
+---
+
+### 2. CPM (Counts Per Million mapped reads)
+
+**Formula:** `(Number of reads) / (Total mapped reads in millions)`
+
+**Also known as:** RPM (Reads Per Million)
+
+**When to use:**
+- Comparing the same genomic regions across different samples
+- When region length is constant or not relevant
+- ChIP-seq, ATAC-seq, DNase-seq analyses
+
+**Available in:** `bamCoverage`, `bamCompare`
+
+**Example:**
+```bash
+bamCoverage --bam input.bam --outFileName output.bw \
+    --normalizeUsing CPM
+```
+
+**Interpretation:** CPM of 5 means 5 reads per million mapped reads in that bin.
+
+**Pros:**
+- Simple and intuitive
+- Good for comparing samples with different sequencing depths
+- Appropriate when comparing fixed-size bins
+
+**Cons:**
+- Does not account for region length
+- Affected by highly abundant regions (e.g., rRNA in RNA-seq)
+
+---
+
+### 3. BPM (Bins Per Million mapped reads)
+
+**Formula:** `(Number of reads in bin) / (Sum of all reads in bins in millions)`
+
+**Key difference from CPM:** Only considers reads that fall within the analyzed bins, not all mapped reads.
+
+**When to use:**
+- Similar to CPM, but when you want to exclude reads outside analyzed regions
+- Comparing specific genomic regions while ignoring background
+
+**Available in:** `bamCoverage`, `bamCompare`
+
+**Example:**
+```bash
+bamCoverage --bam input.bam --outFileName output.bw \
+    --normalizeUsing BPM
+```
+
+**Interpretation:** BPM accounts only for reads in the binned regions.
+
+**Pros:**
+- Focuses normalization on analyzed regions
+- Less affected by reads in unanalyzed areas
+
+**Cons:**
+- Less commonly used, may be harder to compare with published data
+
+---
+
+### 4. RPGC (Reads Per Genomic Content)
+
+**Formula:** `(Number of reads × Scaling factor) / Effective genome size`
+
+**Scaling factor:** Calculated to achieve 1× genomic coverage (1 read per base)
+
+**When to use:**
+- Want comparable coverage values across samples
+- Need interpretable absolute coverage values
+- Comparing samples with very different total read counts
+- ChIP-seq with spike-in normalization context
+
+**Available in:** `bamCoverage`, `bamCompare`
+
+**Requires:** `--effectiveGenomeSize` parameter
+
+**Example:**
+```bash
+bamCoverage --bam input.bam --outFileName output.bw \
+    --normalizeUsing RPGC \
+    --effectiveGenomeSize 2913022398
+```
+
+**Interpretation:** Signal value approximates the coverage depth (e.g., value of 2 ≈ 2× coverage).
+
+**Pros:**
+- Produces 1× normalized coverage
+- Interpretable in terms of genomic coverage
+- Good for comparing samples with different sequencing depths
+
+**Cons:**
+- Requires knowing effective genome size
+- Assumes uniform coverage (not true for ChIP-seq with peaks)
+
+---
+
+### 5. None (No Normalization)
+
+**Formula:** Raw read counts
+
+**When to use:**
+- Preliminary analysis
+- When samples have identical library sizes (rare)
+- When downstream tool will perform normalization
+- Debugging or quality control
+
+**Available in:** All tools (usually default)
+
+**Example:**
+```bash
+bamCoverage --bam input.bam --outFileName output.bw \
+    --normalizeUsing None
+```
+
+**Interpretation:** Raw read counts per bin.
+
+**Pros:**
+- No assumptions made
+- Useful for seeing raw data
+- Fastest computation
+
+**Cons:**
+- Cannot fairly compare samples with different sequencing depths
+- Not suitable for publication figures
+
+---
+
+### 6. SES (Selective Enrichment Statistics)
+
+**Method:** Signal Extraction Scaling - more sophisticated method for comparing ChIP to control
+
+**When to use:**
+- ChIP-seq analysis with bamCompare
+- Want sophisticated background correction
+- Alternative to simple readCount scaling
+
+**Available in:** `bamCompare` only
+
+**Example:**
+```bash
+bamCompare -b1 chip.bam -b2 input.bam -o output.bw \
+    --scaleFactorsMethod SES
+```
+
+**Note:** SES is specifically designed for ChIP-seq data and may work better than simple read count scaling for noisy data.
+
+---
+
+### 7. readCount (Read Count Scaling)
+
+**Method:** Scale by ratio of total read counts between samples
+
+**When to use:**
+- Default for `bamCompare`
+- Compensating for sequencing depth differences in comparisons
+- When you trust that total read counts reflect library size
+
+**Available in:** `bamCompare`
+
+**Example:**
+```bash
+bamCompare -b1 treatment.bam -b2 control.bam -o output.bw \
+    --scaleFactorsMethod readCount
+```
+
+**How it works:** If sample1 has 100M reads and sample2 has 50M reads, sample2 is scaled by 2× before comparison.
+
+---
+
+## Normalization Method Selection Guide
+
+### For ChIP-seq Coverage Tracks
+
+**Recommended:** RPGC or CPM
+
+```bash
+bamCoverage --bam chip.bam --outFileName chip.bw \
+    --normalizeUsing RPGC \
+    --effectiveGenomeSize 2913022398 \
+    --extendReads 200 \
+    --ignoreDuplicates
+```
+
+**Reasoning:** Accounts for sequencing depth differences; RPGC provides interpretable coverage values.
+
+---
+
+### For ChIP-seq Comparisons (Treatment vs Control)
+
+**Recommended:** log2 ratio with readCount or SES scaling
+
+```bash
+bamCompare -b1 chip.bam -b2 input.bam -o ratio.bw \
+    --operation log2 \
+    --scaleFactorsMethod readCount \
+    --extendReads 200 \
+    --ignoreDuplicates
+```
+
+**Reasoning:** Log2 ratio shows enrichment (positive) and depletion (negative); readCount adjusts for depth.
+
+---
+
+### For RNA-seq Coverage Tracks
+
+**Recommended:** CPM or RPKM
+
+```bash
+# Strand-specific forward
+bamCoverage --bam rnaseq.bam --outFileName forward.bw \
+    --normalizeUsing CPM \
+    --filterRNAstrand forward
+
+# For gene-level: RPKM accounts for gene length
+bamCoverage --bam rnaseq.bam --outFileName output.bw \
+    --normalizeUsing RPKM
+```
+
+**Reasoning:** CPM for comparing fixed-width bins; RPKM for genes (accounts for length).
+
+---
+
+### For ATAC-seq
+
+**Recommended:** RPGC or CPM
+
+```bash
+bamCoverage --bam atac_shifted.bam --outFileName atac.bw \
+    --normalizeUsing RPGC \
+    --effectiveGenomeSize 2913022398
+```
+
+**Reasoning:** Similar to ChIP-seq; want comparable coverage across samples.
+
+---
+
+### For Sample Correlation Analysis
+
+**Recommended:** CPM or RPGC
+
+```bash
+multiBamSummary bins \
+    --bamfiles sample1.bam sample2.bam sample3.bam \
+    -o readCounts.npz
+
+plotCorrelation -in readCounts.npz \
+    --corMethod pearson \
+    --whatToShow heatmap \
+    -o correlation.png
+```
+
+**Note:** `multiBamSummary` doesn't explicitly normalize, but correlation analysis is robust to scaling. For very different library sizes, consider normalizing BAM files first or using CPM-normalized bigWig files with `multiBigwigSummary`.
+
+---
+
+## Advanced Normalization Considerations
+
+### Spike-in Normalization
+
+For experiments with spike-in controls (e.g., *Drosophila* chromatin spike-in for ChIP-seq):
+
+1. Calculate scaling factors from spike-in reads
+2. Apply custom scaling factors using `--scaleFactor` parameter
+
+```bash
+# Calculate spike-in factor (example: 0.8)
+SCALE_FACTOR=0.8
+
+bamCoverage --bam chip.bam --outFileName chip_spikenorm.bw \
+    --scaleFactor ${SCALE_FACTOR} \
+    --extendReads 200
+```
+
+---
+
+### Manual Scaling Factors
+
+You can apply custom scaling factors:
+
+```bash
+# Apply 2× scaling
+bamCoverage --bam input.bam --outFileName output.bw \
+    --scaleFactor 2.0
+```
+
+---
+
+### Chromosome Exclusion
+
+Exclude specific chromosomes from normalization calculations:
+
+```bash
+bamCoverage --bam input.bam --outFileName output.bw \
+    --normalizeUsing RPGC \
+    --effectiveGenomeSize 2913022398 \
+    --ignoreForNormalization chrX chrY chrM
+```
+
+**When to use:** Sex chromosomes in mixed-sex samples, mitochondrial DNA, or chromosomes with unusual coverage.
+
+---
+
+## Common Pitfalls
+
+### 1. Using RPKM for bin-based data
+**Problem:** RPKM accounts for region length, but all bins are the same size
+**Solution:** Use CPM or RPGC instead
+
+### 2. Comparing unnormalized samples
+**Problem:** Sample with 2× sequencing depth appears to have 2× signal
+**Solution:** Always normalize when comparing samples
+
+### 3. Wrong effective genome size
+**Problem:** Using hg19 genome size for hg38 data
+**Solution:** Double-check genome assembly and use correct size
+
+### 4. Ignoring duplicates after GC correction
+**Problem:** Can introduce bias
+**Solution:** Never use `--ignoreDuplicates` after `correctGCBias`
+
+### 5. Using RPGC without effective genome size
+**Problem:** Command fails
+**Solution:** Always specify `--effectiveGenomeSize` with RPGC
+
+---
+
+## Normalization for Different Comparisons
+
+### Within-sample comparisons (different regions)
+**Use:** RPKM (accounts for region length)
+
+### Between-sample comparisons (same regions)
+**Use:** CPM, RPGC, or BPM (accounts for library size)
+
+### Treatment vs Control
+**Use:** bamCompare with log2 ratio and readCount/SES scaling
+
+### Multiple samples correlation
+**Use:** CPM or RPGC normalized bigWig files, then multiBigwigSummary
+
+---
+
+## Quick Reference Table
+
+| Method | Accounts for Depth | Accounts for Length | Best For | Command |
+|--------|-------------------|---------------------|----------|---------|
+| RPKM | ✓ | ✓ | RNA-seq genes | `--normalizeUsing RPKM` |
+| CPM | ✓ | ✗ | Fixed-size bins | `--normalizeUsing CPM` |
+| BPM | ✓ | ✗ | Specific regions | `--normalizeUsing BPM` |
+| RPGC | ✓ | ✗ | Interpretable coverage | `--normalizeUsing RPGC --effectiveGenomeSize X` |
+| None | ✗ | ✗ | Raw data | `--normalizeUsing None` |
+| SES | ✓ | ✗ | ChIP comparisons | `bamCompare --scaleFactorsMethod SES` |
+| readCount | ✓ | ✗ | ChIP comparisons | `bamCompare --scaleFactorsMethod readCount` |
+
+---
+
+## Further Reading
+
+For more details on normalization theory and best practices:
+- deepTools documentation: https://deeptools.readthedocs.io/
+- ENCODE guidelines for ChIP-seq analysis
+- RNA-seq normalization papers (DESeq2, TMM methods)