MACS2_BDGDIFF(1)

💖 MACS2_BDGDIFF 💖

okay bestie, sit down, hydrate, and let me tell you about macs2_bdgdiff — it's the macs2 bdgdiff command, and no cap it is the tool for spotting which regions of your genome are living different lives in two different conditions. This page is the manual for it, so let's get into it. 🦋

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🌸 NAME 🌸

macs2_bdgdiff — Model-based Analysis for ChIP-Sequencing

like, the whole point. model-based. analysis. for. ChIP-Seq. periodt. 👑

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✨ DESCRIPTION ✨

here's the whole vibe of how you call it, fr fr:

usage: macs2 bdgdiff [-h] --t1 T1BDG --t2 T2BDG --c1 C1BDG --c2 C2BDG
       [-C CUTOFF] [-l MINLEN] [-g MAXGAP] [--d1 DEPTH1]
       [--d2 DEPTH2] [--outdir OUTDIR] (--o-prefix OPREFIX | -o OFILE
       OFILE OFILE)

so basically: you hand it two pileup bedGraphs, you hand it two control lambda bedGraphs, and it goes off comparing them. the four --t1/--t2/--c1/--c2 ones are the moment, they are REQUIRED, there is no skipping them. 🫶

🎀 options: 🎀

the way that every single flag is about to be explained to you. don't skip, iykyk.

• -h, --help — shows this help message and dips. that's it, that's the whole job. 💅
• --t1 T1BDG — MACS pileup bedGraph for condition 1. > ⚠️ Incompatible with callpeak --SPMR output. REQUIRED — no --t1, no diffing, sorry bestie. 😭
• --t2 T2BDG — MACS pileup bedGraph for condition 2. > ⚠️ Also incompatible with callpeak --SPMR output. REQUIRED. 🌸
• --c1 C1BDG — MACS control lambda bedGraph for condition 1. > ⚠️ Incompatible with callpeak --SPMR output. REQUIRED. this is the control-side energy for sample one. ✨
• --c2 C2BDG — MACS control lambda bedGraph for condition 2. > ⚠️ Incompatible with callpeak --SPMR output. REQUIRED. and this is sample two's control energy. 🦋
• -C CUTOFF, --cutoff CUTOFF — the logLR cutoff. DEFAULT: 3 (which is a likelihood ratio of 1000, for the math girlies 🔥).
• -l MINLEN, --min-len MINLEN — minimum length of a differential region. wanna yeet the tiny little regions? try a bigger value. DEFAULT: 200.
• -g MAXGAP, --max-gap MAXGAP — maximum gap for merging nearby differential regions together. if you're working with broad marks, consider a wider gap (they get lonely otherwise 🥺). > ⚠️ maximum gap should be smaller than minimum length (-g). DEFAULT: 100.
• --d1 DEPTH1, --depth1 DEPTH1 — sequencing depth (that's # of non-redundant reads in million) for condition 1. it gets used together with --d2, and the description for --d2 below explains how to assign them. Default: 1.
• --d2 DEPTH2, --depth2 DEPTH2 — sequencing depth (again: # of non-redundant reads in million) for condition 2. it gets used together with --d1. DEPTH1 and DEPTH2 are used to calculate a scaling factor for each sample, so the bigger sample gets down-scaled to the level of the smaller one. for example, while comparing 10 million condition 1 and 20 million condition 2, use --d1 10 --d2 20, and then the pileup value in the bedGraph for condition 2 will be divided by 2. Default: 1. math ate, honestly. ➗✨
• --outdir OUTDIR — if you specify it, all output files get written into that directory instead. Default: the current working directory.
• --o-prefix OPREFIX — output file prefix. the actual files will be named as PREFIX_cond1.bed, PREFIX_cond2.bed and PREFIX_common.bed. > ⚠️ mutually exclusive with -o/--ofile — you pick ONE, bestie, you can't have both. 🙈
• -o OFILE OFILE OFILE, --ofile OFILE OFILE OFILE — output filenames. you MUST give three arguments, in order:
  1. file for unique regions in condition 1
  2. file for unique regions in condition 2
  3. file for common regions in both conditions

⚠️ Note: mutually exclusive with --o-prefix. also, three. not one, not two. three. 👑

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and that's the whole page, bestie. no notes, iconic behavior, go find your differential regions. 💜

this was macs2 bdgdiff version 2.2.7.1, from April 2022 — slay, happy diffing, mwah! 💖✨🎀🌈⭐💅