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cut-and-run-tag

separate

Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

When to use

• calling peaks from CUT&RUN/CUT&Tag
• scaling by E. coli spike-in carryover
• choosing SEACR norm mode
• comparing CUT&RUN/Tag results to traditional ChIP
• handling pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences
• IgG-only control logic
• characteristic fragment-size signatures
• lower depth requirements

When not to use

• traditional ChIP analysis

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