MAC3_BDGDIFF(1)

💖 MAC3_BDGDIFF(1) 💖

ok so bestie, welcome to mac3_bdgdiff — that's the Model-based Analysis for ChIP-Sequencing tool, living in the User Commands section of your manual. it's giving differential binding analysis and honestly? iconic. let's get into it 🦋

---

✨ NAME ✨

mac3_bdgdiff — Model-based Analysis for ChIP-Sequencing 🌸

no like literally that's the whole name section. short king. periodt.

---

💅 DESCRIPTION 💅

so here's the usage, and bestie please look at it carefully because there is a LOT going on:

macs3 bdgdiff [-h] --t1 T1BDG --t2 T2BDG --c1 C1BDG --c2 C2BDG
       [-C CUTOFF] [-l MINLEN] [-g MAXGAP] [--d1 DEPTH1]
              [--d2 DEPTH2] [--verbose VERBOSE] [--outdir OUTDIR] (--o-prefix
              OPREFIX | -o OFILE OFILE OFILE)

okay the vibe: you feed it two conditions' pileup bedGraphs plus two control lambda bedGraphs, and it finds the regions that are actually different between them. main character energy fr fr. 🔥

🎀 options 🎀

• -h, --help — show this help message and exit. the universal "help me bestie" button. 🙈
• --t1 T1BDG — MACS pileup bedGraph for condition 1. Incompatible with callpeak --SPMR output. ⚠️ REQUIRED — like, you cannot skip this one, she's mandatory.
• --t2 T2BDG — MACS pileup bedGraph for condition 2. Incompatible with callpeak --SPMR output. ⚠️ REQUIRED
• --c1 C1BDG — MACS control lambda bedGraph for condition 1. Incompatible with callpeak --SPMR output. ⚠️ REQUIRED
• --c2 C2BDG — MACS control lambda bedGraph for condition 2. Incompatible with callpeak --SPMR output. ⚠️ REQUIRED

ok real talk, all four of these are REQUIRED and all four are incompatible with callpeak --SPMR output. that is not a suggestion, that is the law. 💀

• -C, --cutoff CUTOFF — log10LR cutoff. regions with signals lower than the cutoff will not be considered as enriched regions (yes, the original says "considerred", we love a typo, we keep the meaning). DEFAULT: 3 (which = likelihood ratio of 1000, math girlie math 🤓)
• -l, --min-len MINLEN — minimum length of a differential region. try a bigger value to remove those tiny little regions you don't care about. DEFAULT: 200
• -g, --max-gap MAXGAP — maximum gap used to merge nearby differential regions. for broad marks, consider a wider gap. ⚠️ maximum gap should be smaller than minimum length (-g). DEFAULT: 100
• --d1, --depth1 DEPTH1 — sequencing depth (# of non-redundant reads, in millions) for condition 1. it gets used together with --d2. see the --d2 description right below for how to assign them. Default: 1
• --d2, --depth2 DEPTH2 — sequencing depth (# of non-redundant reads, in millions) 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. example time bestie: if you're comparing 10 million for condition 1 against 20 million for condition 2, you'd run --d1 10 --d2 20, and then the pileup value in the bedGraph for condition 2 gets divided by 2. 🧮✨ Default: 1
• --verbose VERBOSE — sets the verbose level of runtime messages. the levels, in order:
  • 0: only show critical messages
  • 1: show additional warning messages
  • 2: show process information
  • 3: show debug messages

DEFAULT:2 — so yes, she's chatty by default. 💬

• --outdir OUTDIR — if specified, all output files get written to that directory. Default: the current working directory
• --o-prefix OPREFIX — output file prefix. the actual files will be named PREFIX_cond1.bed, PREFIX_cond2.bed and PREFIX_common.bed. mutually exclusive with -o/--ofile — pick one, not both, you can't have two mains. 🚫
• -o, --ofile OFILE OFILE OFILE — output filenames. you must give three arguments, in this 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. 🌈

---

and that's the whole page bestie, you ate that. this was macs3 bdgdiff version 3.0.4, from May 2026 — go forth and diff some binding sites, ily, mwah 💜🎀🫶