Version Compatibility

Reference examples tested with: MACS2 2.2+, MACS3 3.0+, HOMER 4.11+

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

• 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.

Peak Calling

"Call peaks from my ChIP-seq data" → Identify significantly enriched regions (narrow peaks for TFs, broad peaks for histone marks) by comparing IP signal to input control.

• CLI (MACS3): macs3 callpeak -t chip.bam -c input.bam -f BAM -g hs -n sample
• CLI (HOMER): makeTagDirectory tags/ chip.bam then findPeaks tags/ -style factor -i input_tags/ -o peaks.txt

Choosing a Peak Caller

MACS3 and HOMER use fundamentally different statistical approaches. MACS3 builds a dynamic local Poisson model (taking the maximum of genome-wide, 1kb, 5kb, and 10kb background estimates). HOMER applies three independent sequential filters: control enrichment, local enrichment, and clonal signal complexity. Neither is universally superior — the choice depends on the analysis context.