MAC3_BDGOPT(1)

💖 MAC3_BDGOPT(1) 💖

okay bestie, gather round, because we're talking about mac3_bdgopt (that's a User Commands situation, the <hotpink>Model-based Analysis for ChIP-Sequencing</hotpink> girlies) and honestly? she's a little niche but she ATE. 🧬✨

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🌸 NAME 🌸

mac3_bdgopt — Model-based Analysis for ChIP-Sequencing

like yes, that's the whole name section, she's mysterious, she's lowkey. moving on. 💅

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🦋 DESCRIPTION 🦋

so the vibe here is that you call her like this, fr fr:

usage: macs3 bdgopt [-h] -i IFILE [-m {multiply,add,p2q,max,min}]
       [-p [EXTRAPARAM ...]] [--outdir OUTDIR] -o OFILE
       [--verbose VERBOSE]

and she takes your bedGraph and she does stuff to it. that's the whole plot. no cap. 🎀

✨ options: ✨

• -h, --help — shows this help message and then dips. classic. exit stage left. 🫶
• -i, --ifile _IFILE_ — your MACS score in bedGraph. ⚠️ IMPORTANT NOTE GIRL ⚠️ this bedGraph has to cover the ENTIRE genome. the whole thing. not a corner of it, not "most of it", the ENTIRE. genome. and yeah she's REQUIRED, so don't come to the function empty-handed. 💀
• -m, --method {multiply,add,p2q,max,min} — the method for modifying the score column of your bedGraph file. the available choices are literally: multiply, add, max, min, or p2q. let me break it down for you one by one because she has RANGE:
  1. multiply — the EXTRAPARAM is required and it gets multiplied into the score column. and listen, if your brain wants to divide the score column by X? you use the value 1/X as your EXTRAPARAM. that's the hack. iykyk. 🌈
  2. add — the EXTRAPARAM is required and it gets added to the score column. wanna subtract the score column by X instead? use -X as the EXTRAPARAM. simple as that bestie. 💜
  3. max — the EXTRAPARAM is required and she takes the maximum value between the score and the EXTRAPARAM. taking the bigger one, as she should. 👑
  4. min — the EXTRAPARAM is required and she takes the minimum value between the score and the EXTRAPARAM. humble. demure. the smaller one. 🙈
  5. p2q — this one converts p-value scores to q-value scores using the Benjamini-Hochberg process. the EXTRAPARAM is not required here, she's self-sufficient. ⚠️ BUT ⚠️ this method assumes the scores are -log10 p-value from MACS3. any other type of score will cause unexpected errors. do not test her. do not. 😭
• -p, --extra-param [EXTRAPARAM ...] — the extra parameter for your METHOD. go read the details of the -m option above, i literally just explained it, bestie. 🍓
• --outdir _OUTDIR_ — if you specify this, all output files get written to that directory. if you don't? Default: the current working directory, which is where you already are, living your life. 🦋
• -o, --ofile _OFILE_ — output BEDGraph filename. yes you have to give her one. ✨
• --verbose _VERBOSE_ — sets the verbose level of runtime messages, aka how chatty she is:
  • 0 — only show critical message (silent queen, main character energy)
  • 1 — show additional warning message
  • 2 — show process information
  • 3 — show debug messages (she's telling you EVERYTHING)

DEFAULT: 2. she's a talker by default. 💅

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real talk though bestie: that -i file is REQUIRED, the -m methodology matters a LOT for your output, and if you're doing p2q with the wrong kind of scores you're gonna have a bad time. check your inputs. i love you. 🫶

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and that's the whole page, fr fr — this was macs3 bdgopt version <purple>3.0.4</purple> dated <lavender>May 2026</lavender>, from your girl MAC3_BDGOPT(1). slay, bye, go process some bedGraphs. 💖✨🎀🦋🌸💅