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differential-accessibility

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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.

When to use

• comparing ATAC-seq accessibility between treatment groups
• choosing between consensus-peak vs sliding-window approaches
• picking the correct normalization (full library vs reads-in-peaks)
• correcting batch with SVA/RUVseq
• interpreting log2FC and FDR thresholds in a chromatin context
• identifying differentially accessible chromatin regions
• building a sample-by-region count matrix
• fitting a generalized linear model (negative-binomial)

When not to use

• single-cell ATAC pseudobulk
• allele-specific accessibility
• plant / non-model organism annotation

Skill page

Source