MACS2_RANDSAMPLE(1)

✨ NAME ✨

macs2_randsample — Model-based Analysis for ChIP-Sequencing 💖

(it's the randsample subcommand of MACS2, bestie, and yes the manual page is literally called MACS2_RANDSAMPLE(1) 🎀)

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🌸 DESCRIPTION 🌸

okay so you wanna down-sample your tag files? that's literally what this is for. here's the vibe:

macs2 randsample [-h] -i IFILE [IFILE ...] (-p PERCENTAGE | -n NUMBER)
                 [--seed SEED] [-o OUTPUTFILE] [--outdir OUTDIR]
                 [-s TSIZE]
                 [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}]
                 [--buffer-size BUFFER_SIZE] [--verbose VERBOSE]

that's the whole mood. let's break it down 👑

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💅 options:

• -h, --help — show this help message and exit. iconic behavior, honestly. use it when you're lost. 🫶
• -i IFILE [IFILE ...], --ifile IFILE [IFILE ...] — Alignment file. If multiple files are given as '-t A B C', then they will all be read and combined. Note that pair-end data is not supposed to work with this command. REQUIRED. 🚨

lowkey important: pair-end data is not supposed to work here. don't come for me, I'm just the messenger 😭

• -p PERCENTAGE, --percentage PERCENTAGE — Percentage of tags you want to keep. Input 80.0 for 80%. This option can't be used at the same time with -n/--num. REQUIRED ✨
• -n NUMBER, --number NUMBER — Number of tags you want to keep. Input 8000000 or 8e+6 for 8 million. This option can't be used at the same time with -p/--percent. Note that the number of tags in output is approximate as the number specified here. REQUIRED 💯

so pick a lane bestie: -p or -n. not both. the two options are literally beefing 🥊

• --seed SEED — Set the random seed while down sampling data. Must be a non-negative integer in order to be effective. DEFAULT: not set 🌱
• -o OUTPUTFILE, --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 🦋
• --outdir OUTDIR — If specified all output files will be written to that directory. Default: the current working directory 📁
• -s TSIZE, --tsize TSIZE — Tag size. This will override the auto detected tag size. DEFAULT: Not set 📏
• -f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}, --format {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE} — Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or "SAM" or "BAM" or "BOWTIE" or "BAMPE" or "BEDPE". The default AUTO option will macs2 randsample decide which format the file is. Please check the definition in README file if you choose ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE or BAMPE/BEDPE. 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 🧠

the way that smaller buffer = less RAM but slower reads… it's giving tradeoff, fr fr ⚖️

• --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 🔊

if you're hunting duplicate reads, crank it to 3 and watch the drama unfold 💀

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and that's the whole page, bestie 🎀 go forth and down-sample responsibly ✨

macs2 randsample 2.2.7.1 — April 2022 — page MACS2_RANDSAMPLE(1) 💜 bye ily, read your README, drink water 🫶🌸