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peak-calling

separate

Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

When to use

• calling peaks from ChIP-seq alignments
• choosing between narrow vs broad mode
• deciding model vs nomodel for low-depth data
• applying ENCODE pseudoreplicate IDR
• reconciling MACS vs HOMER vs SPP results
• handling input control matching
• fragment-size modeling
• aligner-specific shifts

When not to use

• CUT&RUN / CUT&Tag peak calling
• ATAC-seq peak calling
• antibody validation
• fragment-size distribution rescue

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