MACS2_PILEUP(1)

💖 macs2_pileup 💖

okay bestie, listen up — this is the manual page for macs2_pileup, aka the pileup era of Model-based Analysis for ChIP-Sequencing (MACS2, you know her, you love her). no cap, she's iconic. let's get into it 🧚✨

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🌸 NAME 🌸

macs2_pileup — Model-based Analysis for ChIP-Sequencing 💅

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🦋 DESCRIPTION 🦋

here's the vibe check, the literal usage line, copy it exactly bestie:

usage: macs2 pileup [-h] -i IFILE [IFILE ...] -o OUTPUTFILE [--outdir OUTDIR]

       [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
              [-B] [--extsize EXTSIZE] [--buffer-size BUFFER_SIZE] [--verbose VERBOSE]

that's the whole energy of this command right there. no notes. 👑

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✨ options ✨

• -h, --help — shows this help message and then dips. classic. 🙈
• -i IFILE [IFILE ...], --ifile IFILE [IFILE ...] — the alignment file(s), bestie. if you hand over multiple files like -t A B C, they all get read and combined. ⚠️ heads up though: pair-end data is not supposed to work with this command, like at all, so don't come for me. this one is REQUIRED.
• -o OUTPUTFILE, --ofile OUTPUTFILE — the name of the output bedGraph file. if you don't specify it, it writes to standard output instead. either way, REQUIRED. 🫶
• --outdir OUTDIR — if you specify this, all the output files get written into that directory. Default: the current working directory. it's giving "put it where I say" 💖
• -f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}, --format {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE} — format of the tag file, and the options are literally "AUTO", "BED", "ELAND", "ELANDMULTI", "ELANDEXPORT", "SAM", "BAM", "BOWTIE", "BAMPE", or "BEDPE". the default AUTO option lets macs2 pileup decide which format the file is all by itself (main character energy fr fr). DEFAULT: "AUTO" — MACS2 will pick a format from "AUTO", "BED", "ELAND", "ELANDMULTI", "ELANDEXPORT", "SAM", "BAM" and "BOWTIE". but if the format is BAMPE or BEDPE, please specify it explicitly, she will not guess for you. 📢 and note: when the format is BAMPE or BEDPE, the -B and --extsize options would be ignored.
• -B, --both-direction — okay so by default, any read gets extended towards the downstream direction by extension size. that means it's [0,size-1] (1-based index system) for plus strand read and [-size+1,0] for minus strand read, where position 0 is the 5' end of the aligned read. that default behavior can simulate MACS2's way of piling up ChIP sample reads, where extension size is set as fragment size/d. ✨ now if this option is set as on, aligned reads get extended in both upstream and downstream directions by extension size. that means [-size,size] where 0 is the 5' end of a aligned read. it can partially simulate MACS2's way of piling up control reads. however, MACS2 local bias is calculated by maximizing the expected pileup over a ChIP fragment size/d estimated from 10kb, 1kb, d and whole genome background. this option will be ignored when the format is set as BAMPE or BEDPE. DEFAULT: False 💀
• --extsize EXTSIZE — the extension size in bps. each alignment read will become a EXTSIZE of fragment, then be piled up. check the description for -B for the details, bestie. it's twice the shiftsize in old MACSv1 language (iykyk). this option will be ignored when the format is set as BAMPE or BEDPE. DEFAULT: 200 🌈
• --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 touch this parameter, like genuinely. however, if there are a large number of chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size in order to decrease memory usage (but it will take longer time to read alignment files, so pick your battle 🥲). minimum memory requested for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8 Bytes. DEFAULT: 100000
• --verbose VERBOSE — set the verbose level, queen:
  • 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 👑

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🎀 quick reminder bestie: every option, default, number and flag up there is load-bearing. don't skip them, don't rename them, don't "fix" them. the vibes are mine, the facts are hers. 💜

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and that's the whole page, fr fr. this was macs2 pileup, version 2.2.7.1, dated April 2022 — aka the MACS2_PILEUP(1) era, and yes she ate and left no crumbs. go pile something up, bestie, you've got this 💖✨🦋🌸💅🫶