Version Compatibility

Reference examples tested with: MACS3 3.0+, Subread 2.0+, bedtools 2.31+, deepTools 3.5+, pybedtools 0.9+, pysam 0.22+, samtools 1.19+

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 ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

ChIP-seq Quality Control

"Assess the quality of my ChIP-seq experiment" → Compute FRiP, cross-correlation (NSC/RSC), library complexity, and IDR replicate concordance to evaluate enrichment success.

• CLI: deeptools plotFingerprint, phantompeakqualtools run_spp.R
• Python: pysam + pybedtools for custom QC metrics

Quality metrics for assessing ChIP-seq experiment success and replicate reproducibility.