bio-atac-seq-differential-accessibility

Version Compatibility

Reference examples tested with: DESeq2 1.42+, GenomicRanges 1.54+, Subread 2.0+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scipy 1.12+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Differential Accessibility

"Find differentially accessible regions between my conditions" → Identify chromatin regions with statistically significant changes in accessibility between treatment groups, cell types, or timepoints.

• R: DiffBind or DESeq2 on a peak-by-sample count matrix

DiffBind Workflow

Goal: Identify differentially accessible chromatin regions between experimental conditions.

Approach: Load sample metadata and peak files into DiffBind, count reads in consensus peaks, normalize, define contrasts, and run differential analysis with DESeq2 backend.

library(DiffBind)

# 1. Create sample sheet
samples <- data.frame(
    SampleID = c('ctrl_1', 'ctrl_2', 'treat_1', 'treat_2'),
    Condition = c('control', 'control', 'treated', 'treated'),
    Replicate = c(1, 2, 1, 2),
    bamReads = c('ctrl_1.bam', 'ctrl_2.bam', 'treat_1.bam', 'treat_2.bam'),
    Peaks = c('ctrl_1.narrowPeak', 'ctrl_2.narrowPeak', 'treat_1.narrowPeak', 'treat_2.narrowPeak')
)
write.csv(samples, 'samples.csv', row.names=FALSE)

# 2. Load data
dba <- dba(sampleSheet='samples.csv')

# 3. Count reads
dba <- dba.count(dba)

# 4. Normalize
dba <- dba.normalize(dba)

# 5. Set up contrasts
dba <- dba.contrast(dba, contrast=c('Condition', 'treated', 'control'))

# 6. Differential analysis
dba <- dba.analyze(dba)

# 7. Get results
results <- dba.report(dba)

DiffBind with Consensus Peaks

library(DiffBind)

# Load samples
dba <- dba(sampleSheet='samples.csv')

# Count with specific parameters
dba <- dba.count(dba,
    summits=250,           # Re-center peaks on summit
    minOverlap=2,          # Peak in at least 2 samples
    score=DBA_SCORE_NORMALIZED)

# Normalize
dba <- dba.normalize(dba, normalize=DBA_NORM_NATIVE)

# Analyze
dba <- dba.contrast(dba, contrast=c('Condition', 'treated', 'control'))
dba <- dba.analyze(dba, method=DBA_DESEQ2)

# Extract results
results <- dba.report(dba, th=0.05, bCounts=TRUE)

# Save
write.csv(as.data.frame(results), 'differential_peaks.csv')

DiffBind Visualizations

# PCA plot
dba.plotPCA(dba, attributes=DBA_CONDITION)

# MA plot
dba.plotMA(dba)

# Volcano plot
dba.plotVolcano(dba)

# Heatmap of differential peaks
dba.plotHeatmap(dba, contrast=1, correlations=FALSE)

# Venn diagram of overlapping peaks
dba.plotVenn(dba, contrast=1, bDB=TRUE, bGain=TRUE, bLoss=TRUE)

Using DESeq2 Directly

Goal: Run differential accessibility analysis using DESeq2 on a peak count matrix without DiffBind.

Approach: Load peak-by-sample counts into a DESeqDataSet, filter low counts, run the DESeq2 pipeline, and extract significant differential peaks.

library(DESeq2)
library(GenomicRanges)

# Load peak counts (from featureCounts or custom counting)
counts <- read.delim('peak_counts.txt', row.names=1)

# Sample metadata
coldata <- data.frame(
    row.names = colnames(counts),
    condition = factor(c('control', 'control', 'treated', 'treated'))
)

# Create DESeq object
dds <- DESeqDataSetFromMatrix(countData=counts, colData=coldata, design=~condition)

# Filter low counts
dds <- dds[rowSums(counts(dds)) >= 10, ]

# Run DESeq2
dds <- DESeq(dds)

# Results
res <- results(dds, contrast=c('condition', 'treated', 'control'))
res <- res[order(res$padj), ]

# Significant peaks
sig <- subset(res, padj < 0.05 & abs(log2FoldChange) > 1)

Count Reads in Peaks

Goal: Generate a peak-by-sample count matrix as input for differential analysis.

Approach: Convert consensus peaks to SAF format and run featureCounts to count reads from all BAM files in each peak region.

# Using featureCounts
# First convert peaks to SAF format
awk 'BEGIN{OFS="\t"; print "GeneID\tChr\tStart\tEnd\tStrand"}
     {print $1"_"$2"_"$3, $1, $2, $3, "."}' consensus_peaks.bed > peaks.saf

featureCounts \
    -a peaks.saf \
    -F SAF \
    -o peak_counts.txt \
    -p \
    --countReadPairs \
    -T 8 \
    *.bam

Python Alternative

import pandas as pd
import numpy as np
from scipy import stats

def simple_differential(counts_file, groups):
    '''Simple differential accessibility test.'''
    counts = pd.read_csv(counts_file, sep='\t', index_col=0, comment='#')

    # Normalize to CPM
    cpm = counts.div(counts.sum()) * 1e6

    # Log transform
    log_cpm = np.log2(cpm + 1)

    # Separate groups
    group1 = [c for c in counts.columns if groups[c] == 'control']
    group2 = [c for c in counts.columns if groups[c] == 'treated']

    results = []
    for peak in counts.index:
        g1_vals = log_cpm.loc[peak, group1]
        g2_vals = log_cpm.loc[peak, group2]

        log2fc = g2_vals.mean() - g1_vals.mean()
        t_stat, pval = stats.ttest_ind(g1_vals, g2_vals)

        results.append({
            'peak': peak,
            'log2FoldChange': log2fc,
            'pvalue': pval
        })

    df = pd.DataFrame(results)
    df['padj'] = stats.false_discovery_control(df['pvalue'])

    return df

Annotate Differential Peaks

Goal: Map differential peaks to nearby genes and genomic features for biological interpretation.

Approach: Use ChIPseeker to annotate peaks with promoter/intron/intergenic classification and distance to nearest TSS.

library(ChIPseeker)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)

# Annotate differential peaks
diff_peaks <- dba.report(dba)
peakAnno <- annotatePeak(diff_peaks, TxDb=TxDb.Hsapiens.UCSC.hg38.knownGene)

# Plot annotation
plotAnnoPie(peakAnno)
plotDistToTSS(peakAnno)

# Get genes
genes <- as.data.frame(peakAnno)$geneId

Filter Results

# Get significant results
sig_peaks <- dba.report(dba, th=0.05, fold=1)

# Opened in treatment
opened <- sig_peaks[sig_peaks$Fold > 0]

# Closed in treatment
closed <- sig_peaks[sig_peaks$Fold < 0]

# Export as BED
export.bed(opened, 'opened_peaks.bed')
export.bed(closed, 'closed_peaks.bed')

Multi-factor Designs

# Complex design with batch correction
samples$Batch <- factor(c('A', 'B', 'A', 'B'))

dba <- dba(sampleSheet=samples)
dba <- dba.count(dba)
dba <- dba.normalize(dba)

# Design formula approach
dba <- dba.contrast(dba, design='~Batch + Condition')
dba <- dba.analyze(dba)

Related Skills

• atac-seq/atac-peak-calling - Generate input peaks
• differential-expression/deseq2-basics - DESeq2 methods
• chip-seq/differential-binding - Similar DiffBind workflow
• pathway-analysis/go-enrichment - Analyze differential genes