MACS2_CMBREPS(1)

✨ NAME ✨

macs2_cmbreps — Model-based Analysis for ChIP-Sequencing 💖

okay bestie so this is the manual for macs2_cmbreps, which lives in the MACS2_CMBREPS(1) part of the User Commands world. it's the little helper that squishes multiple replicate score files into one combined score file. and yes, we're doing this together, hand in hand, no cap 🫶

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🌸 DESCRIPTION 🌸

here's the whole vibe, exactly how you'd run it:

usage: macs2 cmbreps [-h] -i IFILE [IFILE ...] [-m {fisher,max,mean}]
       [--outdir OUTDIR] -o OFILE

lowkey that's the entire plot. you feed it a bunch of per-replicate MACS score bedGraphs, you pick how you wanna combine them, and it hands you back one combined BEDGraph. iconic behavior honestly 💅

🎀 options: 🎀

• -h, --help — shows this help message and bails out. the classic. it's giving "just here to read, not to compute" 😌
• -i IFILE [IFILE ...] — MACS score in bedGraph for each replicate. you need at least 2 files, like '-i A B C D'. this one is REQUIRED — like, no skipping it, bestie, the whole thing falls apart without it 🚨
• -m {fisher,max,mean}, --method {fisher,max,mean} — the method used while combining scores from replicates. three flavors, pick your fighter:
  1. fisher — Fisher's combined probability test. it requires scores in ppois form (-log10 pvalues) from bdgcmp. heads up fr fr: any other type of score with this method may cause cmbreps unexpected errors 😭
  2. max — takes the maximum value from replicates at each genomic position. big main character energy, only the strongest survives 👑
  3. mean — takes the average value. democratic, chill, everyone gets a say 🧚

note: except for Fisher's method, max or mean will take scores AS IS — which means they won't convert scores from log scale to linear scale or vice versa. no glow-ups, no transformations, just vibes ✨

• --outdir OUTDIR — if you specify this, all output files get written into that directory instead. Default: the current working directory 📁
• -o OFILE, --ofile OFILE — the output BEDGraph filename for the combined scores. that's the whole point of the operation, so don't forget it 🍓

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and that's the tea, bestie! this page is from macs2 cmbreps version 2.2.7.1, dated April 2022, and it's filed under MACS2_CMBREPS(1) in User Commands. go forth and combine those replicates, you absolute legend 🌈⭐💜