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allele-specific-binding

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Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.

When to use

• identifying variants with allelic effects on TF binding
• fine-mapping causal regulatory variants
• validating deep-learning variant predictions
• characterizing cis-acting regulatory effects
• detecting allele-specific histone modification binding
• cancer copy-number imbalance analysis
• imprinted-locus awareness
• X-inactivation artifact handling

When not to use

• RNA-seq oriented gene-level analysis
• sequence-only deep-learning predictions without chromatin sample

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