MACS3(1)

👑 NAME 👑

hi bestie, meet macs3 — it's Model-based Analysis for ChIP-Sequencing and it's the moment, it's the icon, it's the blueprint 💅 and yes, this whole manual page (the one helpfully titled MACS3(1), under User Commands) is literally about to be your new personality ✨

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🎀 DESCRIPTION 🎀

okay so here's how you even talk to this thing. this is the exact invocation, no cap, copy it character for character:

usage: macs3 [-h] [--version]
             {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak,callvar,hmmratac}
             ...

macs3 — Model-based Analysis for ChIP-Sequencing. that's the whole vibe 🦋

✨ positional arguments ✨

these are your girlies, your roster, the whole squad. pick one. here's the full list, exactly as it comes:

{callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak,callvar,hmmratac}

and now, one by one, because everyone deserves their moment 🫶

• callpeak — the main character of MACS3 fr fr. this one calls peaks from alignment results. like, that's the whole job.
• bdgpeakcall — calls peaks from a bedGraph file. simple. elegant. iconic.
• bdgbroadcall — calls nested broad peaks from a bedGraph file. broad. unbothered. thriving.
• bdgcmp — comparing two signal tracks in bedGraph format. it's giving "spot the difference" but for science 🔥
• bdgopt — operates on the score column of a bedGraph file. just the score column. it knows what it's about 💅
• cmbreps — combines bedGraph files of scores from replicates. group project, but it actually works.
• bdgdiff — differential peak detection based on paired four bedGraph files. yes, four. no, you can't bring three. let it cook.
• filterdup — removes duplicate reads, then saves in a BED/BEDPE format file. decluttering queen 🧚
• predictd — predicts d or fragment size from alignment results. and in the case of PE data, it reports the average insertion/fragment size from all pairs. psychic behaviour, honestly 🔮
• pileup — pileup aligned reads (single-end) or fragments (paired-end). stacking reads like it's a Jenga tower.
• randsample — randomly chooses a number/percentage of total reads, then saves in a BED/BEDPE format file. chaotic good ✨
• refinepeak — takes raw reads alignment, refines peak summits. inspired by SPP. glow-up arc complete 💖
• callvar — calls variants in given peak regions from the alignment BAM files. detective energy 🕵️
• hmmratac — dedicated peak calling based on Hidden Markov Model for ATAC-seq or scATAC-seq data. the specialist. the niche fave. the one who ate and left no crumbs 👑

⭐ options ⭐

just two, bestie, and they're both free real estate:

• -h, --help — shows this help message and exits. your emergency "wait what" button 🙈
• --version — shows the program's version number and exits. so you can flex which era you're on.

and listen — for the command line options of each individual command, you type: macs3 COMMAND -h

that's it. that's the whole "ask your girlie directly" move. lowkey the most useful line on this entire page, ngl 🍓

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okay bestie, go call some peaks. this page ships as macs3 3.0.4, dated May 2026 — so like, remember us when you're famous 👑💜 no cap, fr fr. bye babe, slay 🔥🌸