MACS2_REFINEPEAK(1)

💖 NAME 💖

macs2_refinepeak — the whole thing is called Model-based Analysis for ChIP-Sequencing (yes bestie, that's the MACS in MACS2, we love a glow-up acronym) and this particular lil command is the refinepeak one. It's the macs2 refinepeak subcommand, and this page lives in section 1 of the manual. 🧚

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✨ DESCRIPTION ✨

okay so here's the whole vibe, the literal usage line, no notes:

usage: macs2 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)

that's it, that's the shape of your command. now let's break down every single flag because I would never gatekeep. 🫶

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🎀 OPTIONS 🎀

• -h, --help — shows this help message and dips. classic. 💅
• -b BEDFILE — your candidate peak file, in BED format. REQUIRED. like, you cannot skip this one bestie.
• -i IFILE [IFILE ...], --ifile IFILE [IFILE ...] — your ChIP-seq alignment file. if you hand it multiple files like -t A B C, it reads them ALL and combines them into one. quick heads up tho: pair-end data is not supposed to work with this command, so don't come for me. REQUIRED. obviously.
• -f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}, --format {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE} — the format of your tag file, and your options are literally "AUTO", "BED", "ELAND", "ELANDMULTI", "ELANDEXPORT", "SAM", "BAM", or "BOWTIE". the default AUTO lets macs2 refinepeak figure out the format all by itself (main character behavior fr fr). if you pick ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE, please check the definition in the README file. DEFAULT: "AUTO" ✨
• -c CUTOFF, --cutoff CUTOFF — the cutoff. DEFAULT: 5
• -w WINDOWSIZE, --window-size WINDOWSIZE — scan window size on both sides of the summit (default: 100bp). symmetrical, as it should be. 🌸
• --buffer-size BUFFER_SIZE — buffer size for incrementally increasing the internal array size that stores read alignment info. ngl in most cases you do NOT need to touch this parameter. 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 — the tradeoff being it'll take longer to read alignment files (💀 worth it sometimes). the minimum memory requested for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8 Bytes. DEFAULT: 100000
• --verbose VERBOSE — set the verbose level:
  • 0: only show critical message
  • 1: show additional warning message
  • 2: show process information
  • 3: show debug messages

and if you want to know where the duplicate reads are at? use 3. DEFAULT: 2 🔍

• --outdir OUTDIR — if specified, all output files get written to that directory. Default: the current working directory
• -o OFILE, --ofile OFILE — output file name. mutually exclusive with --o-prefix — pick one, you can't have both. 🙈
• --o-prefix OPREFIX — output file prefix. mutually exclusive with -o/--ofile. same deal, one or the other. ✨

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fr fr bestie, remember: -o/--ofile and --o-prefix are mutually exclusive, -b and -i are both REQUIRED, and pair-end data is not supposed to work here. periodt. 👑

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okay that's the whole page!! this was macs2 refinepeak version 2.2.7.1, dated April 2022, living in manual page MACS2_REFINEPEAK(1). ty for coming to my ted talk, go refine some peaks, ily, slay 💖🦋🌈