MACS2_BDGOPT(1)

✨ NAME ✨

macs2_bdgopt — Model-based Analysis for ChIP-Sequencing 💖

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🦋 DESCRIPTION 🦋

okay so bestie, here's the entire vibe of this one. you call it like this:

usage: macs2 bdgopt [-h] -i IFILE [-m {multiply,add,p2q,max,min}]
              [-p [EXTRAPARAM ...]] [--outdir OUTDIR] -o OFILE

🎀 options 🎀

• -h, --help — shows this help message and then dips. iconic honestly, it's giving "I said what I said."
• -i IFILE, --ifile IFILE — your MACS score in bedGraph. Note: this has to be a bedGraph file covering the ENTIRE genome, like all of it, no skipping. REQUIRED — you literally cannot skip this one, she's mandatory bestie 💅
• -m {multiply,add,p2q,max,min}, --method {multiply,add,p2q,max,min} — the method that does the little makeover on the score column of your bedGraph file. Available choices are: multiply, add, max, min, or p2q. Here's the tea on each one:
  1. multiply — the EXTRAPARAM is required and gets multiplied onto the score column. If you're trying to divide the score column by X, use value of 1/X as EXTRAPARAM. (yes bestie, math girlie hours 🧮✨)
  2. add — the EXTRAPARAM is required and gets added to the score column. If you're trying to subtract the score column by X, use value of -X as EXTRAPARAM. negative numbers ate and left no crumbs.
  3. max — the EXTRAPARAM is required and it takes the maximum value between score and the EXTRAPARAM. biggest one wins, periodt.
  4. min — the EXTRAPARAM is required and it takes the minimum value between score and the EXTRAPARAM. smallest one takes the crown.
  5. p2q — this one converts p-value scores to q-value scores using Benjamini-Hochberg process. the EXTRAPARAM is not required here, she's low maintenance. this method assumes the scores are -log10 p-value from MACS2. any other types of score will cause unexpected errors 💀
• -p [EXTRAPARAM ...], --extra-param [EXTRAPARAM ...] — the extra parameter for METHOD. check the detail of the -m option up there, that's where all the lore lives 🫶
• --outdir OUTDIR — if you specify this, all output files get written to that directory. Default:</> the current working directory. home sweet home fr fr.
• -o OFILE, --ofile OFILE — output BEDGraph filename. give her a name bestie, she deserves one 🌸

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and that's the whole page, no cap 🎀 this was macs2 bdgopt version 2.2.7.1, dated April 2022 — go forth and modify those score columns, you've got this 👑💖