MAC3_BDGPEAKCALL(1)

NAME

mac3_bdgpeakcall — Model-based Analysis for ChIP-Sequencing 💖🧬

DESCRIPTION

okay so bestie, welcome to the mac3_bdgpeakcall page — aka MAC3_BDGPEAKCALL(1) in manpage speak ✨. It's giving "Model-based Analysis for ChIP-Sequencing" energy, and it's literally the tool that calls peaks from your MACS score in bedGraph.

the usage is exactly this, no cap:

usage: macs3 bdgpeakcall [-h] -i IFILE [-c CUTOFF] [-l MINLEN] [-g
       MAXGAP]

       [--cutoff-analysis]
              [--cutoff-analysis-max CUTOFF_ANALYSIS_MAX]
              [--cutoff-analysis-steps CUTOFF_ANALYSIS_STEPS] [--no-trackline]
              [--verbose VERBOSE] [--outdir OUTDIR] (-o OFILE | --o-prefix
              OPREFIX)

---

⚙️ options: ⚙️

• -h, --help — show this help message and exit ✨ (the classic "bestie, explain" move)
• -i, --ifile IFILE — MACS score in bedGraph. REQUIRED 🚨 no cap, you literally cannot skip this one.
• -c, --cutoff CUTOFF — Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS3, score 5 means pvalue 1e-5. Regions with signals lower than cutoff won't be counted as enriched regions. DEFAULT: 5 💅
• -l, --min-length MINLEN — minimum length of peak, better to set it as d value. DEFAULT: 200 👑
• -g, --max-gap MAXGAP — maximum gap between significant points in a peak, better to set it as tag size. DEFAULT: 30 🦋
• --cutoff-analysis — While set, bdgpeakcall will analyze number or total length of peaks that can be called by different cutoff then output a summary table to help user decide a better cutoff. Note, minlen and maxgap may affect the results. DEFAULT: False 💀 the table is lowkey useful, fr fr
• --cutoff-analysis-max CUTOFF_ANALYSIS_MAX — The maximum cutoff score for performing cutoff analysis. Together with --cutoff-analysis-steps, the resolution in the final report can be controlled. Please check the description in --cutoff-analysissteps for detail. DEFAULT: 100 🌈
• --cutoff-analysis-steps CUTOFF_ANALYSIS_STEPS — Steps for performing cutoff analysis. It will be used to decide which cutoff value should be included in the final report. Larger the value, higher resolution the cutoff analysis can be. The cutoff analysis function will first find the smallest (at least 0) and the largest (controlled by --cutoff-analysis-max) score in the data, then break the range of score into CUTOFF_ANALYSIS_STEPS intervals. It will then use each score as cutoff to call peaks and calculate the total number of candidate peaks, the total basepairs of peaks, and the average length of peak in basepair. Please note that the final report ideally should include CUTOFF_ANALYSIS_STEPS rows, but in practice, if the cutoff yield zero peak, the row for that value won't be included. DEFAULT: 100 🧚
• --no-trackline — Tells MACS not to include trackline with bedGraph files. The trackline is used by UCSC for the options for display. 🎀
• --verbose VERBOSE — Set verbose level of runtime message. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. DEFAULT:2 🔥
• --outdir OUTDIR — If specified all output files will be written to that directory. Default: the current working directory 📁
• -o, --ofile OFILE — Output file name. Mutually exclusive with --o-prefix. 💜
• --o-prefix OPREFIX — Output file prefix. Mutually exclusive with -o/--ofile. 🫶

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that's the whole vibe, bestie. go slay some peaks 💅 brought to you by macs3 bdgpeakcall 3.0.4, dated May 2026 🌸