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atacseq-pipeline

separate

Orchestrates the end-to-end bulk ATAC-seq pipeline from FASTQ to differential accessibility and TF footprints, chaining Nextera-aware fastp QC, Bowtie2 alignment, chrM removal, dedup, a single Tn5 +4/-5 shift, MACS3 peak calling, Corces fixed-width consensus, DiffBind/csaw differential accessibility, and TOBIAS footprinting. Use when committing the reference build + blacklist once, recognizing ATAC has NO input control (the shift-extend model IS the background), applying the Tn5 shift exactly once (never combining -f BAMPE with --shift/--extsize), removing chrM before calling, building a fixed-width consensus so per-sample counts are comparable, or choosing MACS3 vs Genrich vs HMMRATAC. Hands mechanism to the atac-seq component skills; not a re-teach of any single step.

When to use

• bulk ATAC-seq pipeline
• FASTQ to differential accessibility
• TF footprints
• Nextera-aware fastp QC
• Bowtie2 alignment
• chrM removal
• dedup
• Tn5 +4/-5 shift

When not to use

• re-teach of any single step
• ChIP-seq analysis
• single-cell ATAC-seq

Skill page

Source