Version Compatibility

Reference examples tested with: Bowtie2 2.5.3+, MACS3 3.0+, bedtools 2.31+, deepTools 3.5+, fastp 0.23+, samtools 1.19+

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

• 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.

ATAC-seq Pipeline

"Run end-to-end ATAC-seq analysis from FASTQ to differential accessibility" → Orchestrate QC, Bowtie2 alignment, MACS3 peak calling, FRiP/TSS enrichment QC, differential accessibility, and optional TOBIAS footprinting.

Complete workflow from raw ATAC-seq FASTQ files to accessibility peaks, differential analysis, and TF footprinting.

Workflow Overview