MAC3_REFINEPEAK(1)

💖 MAC3_REFINEPEAK 💖

okay bestie, welcome to mac3_refinepeak — section 1 of the manual, Model-based Analysis for ChIP-Sequencing era. this is the lil tool that refines your peaks and she EATS. let's get into it 🧚✨

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✨ NAME ✨

mac3_refinepeak — Model-based Analysis for ChIP-Sequencing

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🌸 DESCRIPTION 🌸

here's the vibe, the whole usage situation, literally copied with love so you know exactly how to call her:

usage: macs3 refinepeak [-h] -b BEDFILE -i IFILE [IFILE ...]
       [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}]
       [-c CUTOFF] [-w WINDOWSIZE] [--buffer-size BUFFER_SIZE]
       [--verbose VERBOSE] [--outdir OUTDIR] (-o OFILE | --o-prefix OPREFIX)

🎀 options:

• -h, --help — shows this help message and then dips, exit stage left 💅
• -b BEDFILE — the candidate peak file, in BED format. REQUIRED. no -b, no party. 🙈
• -i, --ifile IFILE [IFILE ...] — your ChIP-seq alignment file. if you hand her multiple files like '-t A B C', she reads them ALL and combines them, no cap. heads up tho: pair-end data is not supposed to work with this command, so don't come for her. REQUIRED. 👑
• -f, --format {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE} — the format of the tag file, and your choices are literally "AUTO", "BED", "ELAND", "ELANDMULTI", "ELANDEXPORT", "SAM", "BAM", or "BOWTIE". the default AUTO option lets 'macs3 refinepeak' figure out which format the file is all by herself (main character detective energy 🔍). if you pick ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE, please check the definition in the README file. DEFAULT: "AUTO"
• -c, --cutoff CUTOFF — the cutoff. regions with SPP wtd score lower than the cutoff will not be considerred (their spelling, not mine, and honestly? iconic of them). DEFAULT: 5
• -w, --window-size WINDOWSIZE — scan window size on both side of the summit (default: 100bp)
• --buffer-size BUFFER_SIZE — buffer size for incrementally increasing internal array size to store reads alignment information. in most cases you don't have to change this parameter, fr fr. BUT — if there are large number of chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size in order to decrease memory usage (tho it will take longer time to read alignment files, tradeoffs bestie 😭). minimum memory requested for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8 Bytes. DEFAULT: 100000
• --verbose VERBOSE — set verbose level. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. if you want to know where are the duplicate reads, use 3. DEFAULT: 2
• --outdir OUTDIR — if specified, all output files will be written to that directory. Default: the current working directory
• -o, --ofile OFILE — output file name. mutually exclusive with --o-prefix. pick ONE, she's not doing both 🫶
• --o-prefix OPREFIX — output file prefix. mutually exclusive with -o/--ofile. again: pick ONE. 💀

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quick vibe check: -b and -i are REQUIRED, and you gotta choose either -o/--ofile or --o-prefix in that little parenthesized group at the end of the usage. the flags said so, not me. ⭐

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this whole thing is macs3 refinepeak version 3.0.4, dated May 2026, and that's the sign-off bestie — go refine those peaks, you're literally the main character, periodt. 💜🦋🌈