MACS2_BDGBROADCALL(1)

💖 MACS2_BDGBROADCALL(1) 💖

okay bestie, gather round, because we're about to talk about macs2_bdgbroadcall — that's the manual page name up there, and this whole thing lives in section 1 of your manual. it's a User Command, it's part of the MACS2 family, and honestly? it's giving broad peak energy. let's get into it 🦋

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✨ NAME ✨

macs2_bdgbroadcall — Model-based Analysis for ChIP-Sequencing. yes that's the whole name, no cap, it's a whole vibe. 🧬

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🌸 DESCRIPTION 🌸

so here's the tea: this is how you call it, fr fr. the usage looks like this:

macs2 bdgbroadcall [-h] -i IFILE [-c CUTOFFPEAK] [-C CUTOFFLINK]
       [-l MINLEN] [-g LVL1MAXGAP] [-G LVL2MAXGAP]
              [--no-trackline] [--outdir OUTDIR] (-o OFILE | --o-prefix
              OPREFIX)

like, look at all those little flags. iconic. every single one of them is doing something, and we're gonna go through them one by one because that's just the kind of friend I am 💅

🎀 options: 🎀

• -h, --help — shows this help message and exits. your little "help me pls" button. so valid. 🙈
• -i IFILE, --ifile IFILE — MACS score in bedGraph. REQUIRED, bestie, like you cannot skip this one. it's the main character of this whole operation. 👑
• -c CUTOFFPEAK, --cutoff-peak CUTOFFPEAK — cutoff for peaks, and which number you want depends on which method you used for the score track. if your file has qvalue scores from MACS2, then score 2 means qvalue 0.01. DEFAULT: 2 ✨
• -C CUTOFFLINK, --cutoff-link CUTOFFLINK — cutoff for linking regions and low abundance regions, and again it depends on the method you used for the score track. if your file has qvalue scores from MACS2, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. DEFAULT: 1 🌈
• -l MINLEN, --min-length MINLEN — minimum length of a peak. the manual says it's better to set it as the d value. DEFAULT: 200 🍓
• -g LVL1MAXGAP, --lvl1-max-gap LVL1MAXGAP — maximum gap between significant peaks. better to set it as the tag size. DEFAULT: 30 🧚
• -G LVL2MAXGAP, --lvl2-max-gap LVL2MAXGAP — maximum linking between significant peaks. better to set it as 4 times the d value. DEFAULT: 800 💜
• --no-trackline — tells MACS not to include the trackline with bedGraph files. and heads up: the trackline is required by UCSC. so like, if you turn it off, that's on you bestie 😭
• --outdir OUTDIR — if you specify this, all your output files get written to that directory. Default: the current working directory 📁
• -o OFILE, --ofile OFILE — output file name. mutually exclusive with --o-prefix, so you literally cannot have both, pick a lane 💀
• --o-prefix OPREFIX — output file prefix. mutually exclusive with -o/--ofile. same deal, choose one 🫶

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quick vibe check reminder: -o/--ofile and --o-prefix are mutually exclusive, so don't try to be greedy and use both. and that --no-trackline thing? UCSC wants the trackline, so removing it is a choice you have to live with. ✨

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and that's the whole page, bestie! this little masterpiece is macs2 bdgbroadcall version 2.2.7.1, dated April 2022. slay, go call some broad peaks, you got this 💖✨🎀