MAC3_PREDICTD(1)

📦
version 3.0.4 · 5 versions
, in ubuntu stonking

💖 MAC3_PREDICTD 💖

okay bestie, welcome to mac3_predictd(1) — yes, section 1, User Commands, we're in the grown-up part of the manual and we're thriving 🫶 This one is all about Model-based Analysis for ChIP-Sequencing, and I'm gonna walk you through every single flag so you never have to squint at --help again. no cap.

🌸 NAME 🌸

mac3_predictd — Model-based Analysis for ChIP-Sequencing ✨

🎀 DESCRIPTION 🎀

here's the vibe, bestie — the usage line is exactly this, don't @ me:

usage: macs3 predictd [-h] -i IFILE [IFILE ...]
       [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
              [-g GSIZE] [-s TSIZE] [--bw BW] [--d-min D_MIN] [-m MFOLD MFOLD]
              [--outdir OUTDIR] [--rfile RFILE] [--buffer-size BUFFER_SIZE]
              [--verbose VERBOSE]

✨ options: ✨

  • -h, --help — shows this help message and then dips. iconic behaviour. 👑
  • -i, --ifile IFILE [IFILE ...] — the ChIP-seq alignment file. if you hand it multiple files like '-t A B C', it reads them all and combines them into one glorious little pile. this one is REQUIRED — no ifile, no ✨. 💅
  • -f, --format {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE} — tells MACS3 what flavour your tag file is: "AUTO", "BED", "ELAND", "ELANDMULTI", "ELANDEXPORT", "SAM", "BAM", "BOWTIE", "BAMPE" or "BEDPE". the default AUTO option lets MACS decide the format for you, so cute. BUT — and this is the important bit, bestie — if you want it to figure out the average insertion size / fragment size from PE data like BEDPE or BAMPE, you gotta say so yourself and specify the format as BAMPE or BEDPE, because MACS3 won't automatically recognize those two formats with -f AUTO. 🙈 also heads up: in PE mode, -g, -s, --bw, --d-min, -m, and --rfile have NO effect. like, zero. none. DEFAULT: "AUTO"
  • -g, --gsize GSIZE — the effective genome size. you can write it as 1.0e+9 or 1000000000, or use the shortcuts: 'hs' for human (2,913,022,398), 'mm' for mouse (2,652,783,500), 'ce' for C. elegans (100,286,401) and 'dm' for fruitfly (142,573,017). Default: hs. those four numbers were collected from Deeptools — https: //deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html — so go peek at deeptools to figure out the best genome size for whatever you're planning to do. 🧬
  • -s, --tsize TSIZE — tag size. this overrides the auto-detected tag size. DEFAULT: Not set
  • --bw BW — band width, aka how wide a region gets picked when it's computing fragment size. note that this value only gets used while the shifting model is being built. DEFAULT: 300
  • --d-min D_MIN — minimum fragment size in basepair. any predicted fragment size that comes in under this gets excluded, sorry babe. DEFAULT: 20
  • -m, --mfold MFOLD MFOLD — picks the regions that fall within the MFOLD range of high-confidence enrichment ratio against background, which is what the model gets built from. fold-enrichment in regions has to be lower than the upper limit and higher than the lower limit. write it like "-m 10 30". DEFAULT: 5 50
  • --outdir OUTDIR — if you specify this, every output file lands in that directory instead. Default: the current working directory
  • --rfile RFILE — the PREFIX of the filename of the R script that draws the X-correlation figure. DEFAULT: 'predictd_model.R' and R file will be predicted_model.R 📈
  • --buffer-size BUFFER_SIZE — buffer size for incrementally bumping up the internal array size that stores read alignment info. in most cases you do not have to touch this, trust. but if your alignment has a huge number of chromosomes/contigs/scaffolds, it's recommended to set a smaller buffer size so you use less memory — the tradeoff is that reading the alignment files will take longer. minimum memory requested for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8 Bytes. DEFAULT: 100000 🧠
  • --verbose VERBOSE — sets how chatty the runtime messages are. 0: only show critical messages, 1: show additional warning messages, 2: show process information, 3: show debug messages. DEFAULT: 2
lowkey reminder: -i/--ifile is REQUIRED, and if you're in PE mode (BAMPE/BEDPE) then -g, -s, --bw, --d-min, -m and --rfile are just decorative. save yourself the confusion bestie 💀

and that's the whole page, bestie!! no notes, we ate 🍓 this was macs3 predictd 3.0.4, dated May 2026 — go forth and predict some fragments, you absolute main character 👑💜

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