MAC3_CMBREPS(1)

💖 MAC3_CMBREPS(1) 💖

okay bestie, so mac3_cmbreps is a lil command from the macs3 family — the Model-based Analysis for Chip-Sequencing situation — and its whole ~thing~ is smashing together the scores from all ur replicates into one big combined score. her full manual-page name is literally MAC3_CMBREPS(1) if ur keeping receipts. 🎀

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✨ NAME ✨

mac3_cmbreps — Model-based Analysis for ChIP-Sequencing 💅

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🌸 SYNOPSIS 🌸

macs3 cmbreps [-h] -i IFILE [IFILE ...] [-m {fisher,max,mean}]
              [--outdir OUTDIR] -o OFILE [--verbose VERBOSE]

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🦋 DESCRIPTION 🦋

so the usage line, queen, goes like this:

usage: macs3 cmbreps [-h] -i IFILE [IFILE ...] [-m {fisher,max,mean}]

       [--outdir OUTDIR] -o OFILE [--verbose VERBOSE]

and then we get into the good stuff 👇

✨ options: ✨

• -h, --help — prints this lil help message and dips out. that's it, that's the whole job 🫶
• -i IFILE [IFILE ...] — the MACS scores in bedGraph, one for each replicate. she needs at least 2 files, like '-i A B C D' — two is the bare minimum, no solo acts allowed. REQUIRED 🔥
• -m, --method {fisher,max,mean} — the method u wanna use while combining scores across replicates. three flavors, pick one:
  1. fisher — Fisher's combined probability test. it needs scores in ppois form (-log10 pvalues) coming from bdgcmp. heads up bestie: other types of scores fed into this method may cause cmbreps unexpected errors 😭 so don't play games with it.
  2. max — takes the maximum value from the replicates at each genomic position. biggest one wins, periodt.
  3. mean — takes the average value. so demure, so balanced.

note: except for Fisher's method, max and mean will take scores AS IS — which means they will not convert scores from log scale to linear scale or vice versa. no sneaky unit conversions here, she takes u at face value 💀

• --outdir OUTDIR — if u specify this, all output files get written into that directory instead. default: the current working directory ✨
• -o, --ofile OFILE — the output BEDGraph filename for the combined scores. this is where ur glorious merged data lands 📁
• --verbose VERBOSE — sets the verbose level of runtime messages. the levels, from quiet to yapper:
  • 0: only show critical message 🙈
  • 1: show additional warning message
  • 2: show process information
  • 3: show debug messages 🐞

DEFAULT: 2 — she's a talker by default, love that for her.

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and that's the whole page, bestie! ur now officially certified in mac3_cmbreps 👑

this manual page is brought to u by macs3 cmbreps version 3.0.4, dated May 2026 — yeah she's serving MAC3_CMBREPS(1) energy and she knows it 💅✨