MACS2(1)

👑 MACS2

macs2 — Model-based Analysis for ChIP-Sequencing 💖

okay bestie, buckle up, because this is the whole macs2 command and it's literally the main character of ChIP-seq analysis. the manual page is MACS2(1), filed under User Commands, and yes we're going through every single subcommand. no skipping. periodt. ✨

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🌸 DESCRIPTION

here's how you even call this thing:

usage: macs2 [-h] [--version]
              {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}
              ...

macs2 — Model-based Analysis for ChIP-Sequencing. that's the whole vibe. 🦋

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🎀 positional arguments

so these are your subcommands, the little besties that actually do the work:

• {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak} — pick one of these, they're all listed right here 💅

and here's what each one does, no gatekeeping:

• callpeak — the Main MACS2 Function: call peaks from alignment results. this is THE one, the icon, the moment. 👑
• bdgpeakcall — call peaks from bedGraph output. ⚠️ note: all regions on the same chromosome in the bedGraph file should be continuous, so only bedGraph files from MACS2 are acceptable. fr fr, don't bring random bedGraphs to this party.
• bdgbroadcall — call broad peaks from bedGraph output. ⚠️ same deal: all regions on the same chromosome in the bedGraph file should be continuous, so only bedGraph files from MACS2 are acceptable. 👯
• bdgcmp — deduct noise by comparing two signal tracks in bedGraph. 🧚 ⚠️ and again: all regions on the same chromosome in the bedGraph file should be continuous, so only bedGraph files from MACS2 are acceptable.
• bdgopt — operations on the score column of a bedGraph file. ✨ ⚠️ you already know: all regions on the same chromosome in the bedGraph file should be continuous, so only bedGraph files from MACS2 are acceptable.
• cmbreps — combine BEDGraphs of scores from replicates. 💖 ⚠️ yep, again: all regions on the same chromosome in the bedGraph file should be continuous, so only bedGraph files from MACS2 are acceptable.
• bdgdiff — differential peak detection based on paired four bedgraph files. 🔥 ⚠️ and (say it with me) all regions on the same chromosome in the bedGraph file should be continuous, so only bedGraph files from MACS2 are acceptable.
• filterdup — remove duplicate reads at the same position, then save the rest of the alignments to a BED or BEDPE file. 🫶 and lowkey a hack: if you use the ' --keep-dup all option', this script can be utilized to convert any acceptable format into BED or BEDPE format. it's giving multitool.
• predictd — predict d or fragment size from alignment results. 🦋 Will NOT filter duplicates — read that again, bestie, it does not filter duplicates. no cap.
• pileup — pileup aligned reads with a given extension size (fragment size, or d in MACS language). 📚 heads up though: there will be no step for duplicate reads filtering or sequencing depth scaling, so you may need to do certain pre/postprocessing. it's a do-it-yourself situation.
• randsample — randomly sample a number/percentage of total reads. 🎲
• refinepeak — (Experimental) take raw reads alignment, refine peak summits and give scores measuring balance of waston/crick tags. Inspired by SPP. 🧪 experimental means experimental, so vibe check it before you trust it with your whole thesis.

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💅 options

• -h, --help — show this help message and exit. the classic escape hatch. 🚪
• --version — show program's version number and exit. 📌

for command line options of each command, type: macs2 COMMAND -h

like, genuinely do that. each subcommand has its own whole world of flags and this page is just the group chat intro. 😭

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anyway, that's the whole page, mwah 💋 — this is macs2 version 2.2.7.1, dated April 2022, and it lives in section MACS2(1). slay, go call some peaks. 🎀🌈✨