Version Compatibility

Reference examples tested with: bedtools 2.31+, samtools 1.19+, BEDOPS 2.4.41+, GenomicRanges 1.54+, DiffBind 3.12+, Subread 2.0.2+ (featureCounts; --countReadPairs requires >= 2.0.2), pybedtools 0.10+.

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 unexpected errors, introspect the installed package and adapt rather than retrying.

Consensus Peakset Construction

"Build a single peakset to count reads against for all my samples" -> Combine per-replicate or per-condition peak calls into a non-redundant, fixed-width set of regions. The strategy chosen drives FDR calibration, peak-width fairness, and reproducibility downstream.

• CLI: bedtools merge (simple union) and bedtools multiinter (per-sample membership columns emitted by default)
• CLI: Corces 2018 iterative overlap removal (custom shell)
• R: DiffBind::dba.count(summits=250) (built-in fixed-width)
• Python: pybedtools for programmatic merging