MAC3_RANDSAMPLE(1)

💖 mac3_randsample — the manual page (yes bestie, we're learning Unix today) 💖

okay so you opened mac3_randsample(1) and you're like "what is this" — don't worry, I got you. Welcome to the group chat version of the man page. No cap, every single flag is staying in here. Let's go ✨

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🌸 NAME 🌸

mac3_randsample — Model-based Analysis for ChIP-Sequencing

(yes that's the whole name section, it's giving short and iconic, we move on 💅)

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🦋 DESCRIPTION 🦋

Here's how you actually call it, in all its glory:

usage: macs3 randsample [-h] -i IFILE [IFILE ...] (-p PERCENTAGE | -n NUMBER)
[--seed SEED] [-o OUTPUTFILE] [--outdir OUTDIR]
[-s TSIZE] [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
[--buffer-size BUFFER_SIZE] [--verbose VERBOSE]

lowkey read that as: you must give input files, and you must pick exactly one of percentage-mode or number-mode. the rest is vibes and tuning. 🫶

✨ options: (the main character section) ✨

• -h, --help — shows this help message and then dips. classic.
• -i, --ifile IFILE [IFILE ...] — your alignment file(s). If you hand it multiple files like -t A B C, it will read them ALL and combine them into one glorious pile. REQUIRED — no input, no party. 😭
• -p, --percentage PERCENTAGE — the percentage of tags you wanna keep. Wanna keep 80%? You type 80.0. Big note: this option can't be used at the same time as -n/--num. And listen, if you set it to 100, it keeps every single read and converts any format MACS3 supports into BED (or BEDPE, if the input is BAMPE) format. REQUIRED (well, unless you're using -n, iykyk)
• -n, --number NUMBER — the number of tags you wanna keep. Type 8000000 or 8e+6 for 8 million, whatever feels right. This one also can't be used at the same time as -p/--percent. Heads up bestie: the number of tags in the output is only approximate to the number you specify here. not exact, just close. 🙈 REQUIRED (unless you're on team -p)
• --seed SEED — sets the random seed while downsampling data. Must be a non-negative integer for it to actually do anything. If you want more reproducible results, please specify a random seed and record it. DEFAULT: not set
• -o, --ofile OUTPUTFILE — output BED file name. If you don't specify it, it writes to standard output. Oh and fyi, if the input format is BAMPE or BEDPE, the output will be in BEDPE format. DEFAULT: stdout
• --outdir OUTDIR — if you specify this, all output files get written to that directory. Default: the current working directory
• -s, --tsize TSIZE — tag size. This one overrides the auto-detected tag size like the queen it is. DEFAULT: Not set
• -f, --format {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE} — format of the tag file. Your choices are "AUTO", "BED", "ELAND", "ELANDMULTI", "ELANDEXPORT", "SAM", "BAM", "BOWTIE", "BAMPE", or "BEDPE". The default AUTO option lets macs3 randsample decide which format the file is. And if you choose ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE or BAMPE/BEDPE, please check the definition in the README file. DEFAULT: "AUTO"
• --buffer-size BUFFER_SIZE — buffer size for incrementally increasing the internal array size used to store reads alignment information. In most cases you truly don't have to touch this parameter, bestie. BUT — if you have a large number of chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size to decrease memory usage. Sneaky tradeoff though: it'll take longer to read alignment files. Minimum memory requested for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8 Bytes. DEFAULT: 100000
• --verbose VERBOSE — sets the verbose level. Like a volume knob but for information:
  • 0: only show critical message
  • 1: show additional warning message
  • 2: show process information
  • 3: show debug messages

And if you're out here wondering where the duplicate reads are at — use 3. 🕵️ DEFAULT: 2

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💀 pro tip from your favorite Unix girlie: -p and -n are NOT friends. pick one. the tool will straight up refuse if you try both.

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and that's the whole page, you ate it, you understood it, periodt. 💅✨

this was macs3 randsample version 3.0.4, from May 2026, and you just finished reading MAC3_RANDSAMPLE(1). go sample some reads bestie, you've got this 🎀🦋🌟