MAC3_FILTERDUP(1)

💖 NAME 💖

mac3_filterdup — Model-based Analysis for ChIP-Sequencing, bestie. That's the manual page mac3_filterdup(1) under User Commands, and she is serving.

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🦋 DESCRIPTION 🦋

okay so here's the whole vibe, the entire invocation, no notes:

usage: macs3 filterdup [-h] -i IFILE [IFILE ...]

       [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
              [-g GSIZE] [-s TSIZE] [-p PVALUE] [--keep-dup KEEPDUPLICATES]
              [--buffer-size BUFFER_SIZE] [--verbose VERBOSE] [--outdir OUTDIR]
              [-o OUTPUTFILE] [-d]

like. she reads your alignment files, she deals with the duplicates, she writes you a clean BED file. main character energy fr fr. 🌸

🎀 options 🎀

• -h, --help — show this help message and exit. the "help me help you" of it all, iconic.
• -i, --ifile IFILE [IFILE ...] — Alignment file. If multiple files are given as '-t A B C', then they will all be read and combined. REQUIRED. yes bestie this one is not optional, you cannot skip it 💅
• -f, --format {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE} — Format of tag file, "AUTO", "BED", "ELAND", "ELANDMULTI", "ELANDEXPORT", "SAM", "BAM", "BOWTIE", "BAMPE", or "BEDPE". The default AUTO option will let MACS3 guess which format the file is. Please check the definition in README file for each specific format. DEFAULT: "AUTO" — she'll clock the format herself if you let her 🔥
• -g, --gsize GSIZE — Effective genome size. It can be 1.0e+9 or 1000000000, or 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. The effective genome size numbers for the above four species are collected from Deeptools https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html. Please refer to deeptools to define the best genome size you plan to use. the shortcuts are lowkey a lifesaver ✨
• -s, --tsize TSIZE — Tag size. This will override the auto detected tag size. DEFAULT: Not set — she autodetects unless you step in 🫶
• -p, --pvalue PVALUE — Pvalue cutoff for binomial distribution test. DEFAULT: 1e-5
• --keep-dup KEEPDUPLICATES — It controls the 'macs3 filterdup' behavior towards duplicate tags/pairs at the exact same location — the same coordination and the same strand. The 'auto' option makes 'macs3 filterdup' calculate the maximum tags at the exact same location based on binomial distribution using given -p as pvalue cutoff; and the 'all' option keeps every tags (useful if you only want to convert formats). If an integer is given, at most this number of tags will be kept at the same location. Note, MACS3 callpeak function uses KEEPDUPLICATES=1 as default. Note, if you've used samtools or picard to flag reads as 'PCR/Optical duplicate' in bit 1024, MACS3 will still read them although the reads may be decided by MACS3 as duplicate later. Default: auto 🧚
• --buffer-size BUFFER_SIZE — Buffer size for incrementally increasing internal array size to store reads alignment information. In most cases, you don't have to change this parameter. However, if there are large number of chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size in order to decrease memory usage (but it will take longer time to read alignment files). Minimum memory requested for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8 Bytes. DEFAULT: 100000
• --verbose VERBOSE — Set verbose level. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. If you want to know where are the duplicate reads, use 3. DEFAULT: 2 — turn it up to 3 if you're nosy about dupes, no judgment
• --outdir OUTDIR — If specified all output files will be written to that directory. Default: the current working directory 🌈
• -o, --ofile OUTPUTFILE — Output BED file name. If not specified, will write to standard output. Note, if the input format is BAMPE or BEDPE, the output will be in BEDPE format. DEFAULT: stdout — no filename? she just yells it right into your terminal, periodt 💅
• -d, --dry-run — When set, filterdup will only output numbers instead of writing output files, including maximum allowable duplicates, total number of reads before filtering, total number of reads after filtering, and redundant rate. Default: not set — a little peek before you commit, we love a test run 🙈

⚠️ heads up bestie: --keep-dup is literally the whole point of this command, so read that one twice before you go keeping every dupe at 'all'. Converting formats is one thing, but you better know why you're doing it. 🔥

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and that's the page!! macs3 filterdup 3.0.4, dated May 2026 — that's the version and the date in the footer, and honestly? she ate. 💖✨ go filter your dupes, you've got this 👑⭐