MAC3_BDGBROADCALL(1)

🌸 MAC3_BDGBROADCALL 🌸

okay bestie, so this is mac3_bdgbroadcall — the Model-based Analysis for ChIP-Sequencing</bold> energy, brought to you as a macs3 subcommand fr fr. 💖

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✨ DESCRIPTION ✨

So like, the way you call it is:

usage: macs3 bdgbroadcall [-h] -i IFILE [-c CUTOFFPEAK] [-C CUTOFFLINK]
       [-l MINLEN] [-g LVL1MAXGAP] [-G LVL2MAXGAP]
              [--no-trackline] [--verbose VERBOSE] [--outdir OUTDIR] (-o OFILE
              | --o-prefix OPREFIX)

that's the whole vibe check right there. now let's get into the options one by one, no skips, no cap 👑

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💅 options 💅

• -h, --help — shows this help message and dips. iconic behavior honestly. ✨
• -i, --ifile IFILE — the MACS score in bedGraph. REQUIRED bestie. you literally cannot skip this one. 🚨
• -c, --cutoff-peak CUTOFFPEAK — the cutoff for peaks, and it depends on which method you used for your score track. so if your file has qvalue scores from MACS3, a score of 2 means qvalue 0.01. and heads up: regions with signals lower than this cutoff won't be considerred as enriched regions. DEFAULT: 2
• -C, --cutoff-link CUTOFFLINK — cutoff for linking regions / low abundance regions, again depending on which method you used for your score track. if the file has qvalue scores from MACS3, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. DEFAULT: 1
• -l, --min-length MINLEN — minimum length of a peak. better to set it as d value. DEFAULT: 200
• -g, --lvl1-max-gap LVL1MAXGAP — maximum gap between significant peaks. better to set it as tag size. DEFAULT: 30
• -G, --lvl2-max-gap LVL2MAXGAP — maximum linking between significant peaks. better to set it as 4 times of d value. DEFAULT: 800
• --no-trackline — tells MACS not to include the trackline with bedGraph files. reminder that the trackline is required by UCSC, so like… know what you're doing here. 🙈
• --verbose VERBOSE — sets the verbose level of runtime messages:
  • 0: only show critical message
  • 1: show additional warning message
  • 2: show process information
  • 3: show debug messages

DEFAULT:2 and honestly 2 is the sweet spot, it's giving main character narration. 🎀

• --outdir OUTDIR — if you specify it, all output files get written to that directory. default is the current working directory. 🗂️
• -o, --ofile OFILE — output file name. mutually exclusive with --o-prefix. you pick one, bestie, not both. 💅
• --o-prefix OPREFIX — output file prefix. mutually exclusive with -o/--ofile. same deal, one or the other. 🦋

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lowkey the whole thing is: give it a bedGraph, tell it your cutoffs, tell it where to write, and it goes off. slay. 👑

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and that's the page babes — macs3 bdgbroadcall version 3.0.4, dated May 2026. periodt. 💖✨🫶