MACS2_BDGPEAKCALL(1)

💖 NAME 💖

macs2_bdgpeakcall — it's the Model-based Analysis for ChIP-Sequencing bestie, and this specific little icon is the one that finds peaks in your bedGraph score file. peak calling, but make it cute 🦋

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✨ DESCRIPTION ✨

okay so here's the whole vibe, fr fr. This is how you run it:

usage: macs2 bdgpeakcall [-h] -i IFILE [-c CUTOFF] [-l MINLEN] [-g
MAXGAP]

[--cutoff-analysis] [--no-trackline]
       [--outdir OUTDIR] (-o OFILE | --o-prefix OPREFIX)

like. you give it a bedGraph of scores, it gives you peaks. that's the main character energy right there 👑

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🎀 options: 🎀

• -h, --help — bestie just show this help message and exit, that's it, that's the whole job 💅
• -i IFILE, --ifile IFILE — MACS score in bedGraph. REQUIRED — not optional, not "maybe later", you literally cannot do this without it, no cap 🚨
• -c CUTOFF, --cutoff CUTOFF — the cutoff depends on which method you used for your score track, so lowkey pay attention here. If the file contains pvalue scores from MACS2, then a score of 5 means pvalue 1e-5. DEFAULT: 5 ⭐
• -l MINLEN, --min-length MINLEN — minimum length of peak, and honestly it's better to set it as the d value. DEFAULT: 200 📏
• -g MAXGAP, --max-gap MAXGAP — maximum gap between significant points in a peak, and yeah better to set it as the tag size. DEFAULT: 30 🫶
• --cutoff-analysis — while this is set, bdgpeakcall will analyze the number or total length of peaks that can be called by different cutoff, then output a summary table to help you decide a better cutoff. note: minlen and maxgap may affect the results, so don't come for me if they do 🙈 DEFAULT: False
• --no-trackline — tells MACS not to include the trackline with bedGraph files. heads up bestie: the trackline is required by UCSC. so like. know what you're doing 💀
• --outdir OUTDIR — if specified, all output files will be written to that directory. Default: the current working directory 🌸
• -o OFILE, --ofile OFILE — output file name. mutually exclusive with --o-prefix, so pick a lane 🎀
• --o-prefix OPREFIX — output file prefix. mutually exclusive with -o/--ofile. same energy, opposite choice ✨

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lowkey the whole thing is just: score file in, peaks out, and don't forget -i or nothing happens 😭

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and that's the tea 🍓 this was macs2 bdgpeakcall version 2.2.7.1, from April 2022 — slay, iconic, periodt. go call some peaks bestie, you've got this 💜🌈👑