MACS2_PREDICTD(1)

💖 MACS2_PREDICTD(1) 💖

okay bestie, welcome to MACS2_PREDICTD — the macs2 predictd manual page, and yes it's literally the whole thing, no skips, no cap 💅

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✨ NAME ✨

macs2_predictd — Model-based Analysis for ChIP-Sequencing 🧬✨

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🌸 DESCRIPTION 🌸

here's how you actually call it, copy-paste energy:

usage: macs2 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]

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🎀 options 🎀

• -h, --help — shows this help message and then dips out (exit). iconic behavior honestly 🫶
• -i IFILE [IFILE ...], --ifile IFILE [IFILE ...] — your ChIP-seq alignment file, the star of the show 👑. If you pass multiple files like -t A B C, they all get read and combined into one big slay. > heads up bestie: pair-end data is not supposed to work with this command, so don't come for me. This one is REQUIRED, periodt.
• -f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE}, --format {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE,BEDPE} — tells MACS what flavor of tag file you're handing over: "AUTO", "BED", "ELAND", "ELANDMULTI", "ELANDEXPORT", "SAM", "BAM", "BOWTIE", "BAMPE" or "BEDPE". The default AUTO option lets MACS decide which format the file is, main character detective energy 🔍. If you choose ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE, please check the definition in the README file, fr fr. DEFAULT: "AUTO"
• -g GSIZE, --gsize GSIZE — the effective genome size 🧬. It can be 1.0e+9 or 1000000000, or you can use the shortcuts: 'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8). Default: hs
• -s TSIZE, --tsize TSIZE — tag size. This overrides the auto detected tag size, so it's giving "I'll take it from here" 💅. DEFAULT: Not set
• --bw BW — band width for picking regions to compute fragment size. This value is only used while building the shifting model. DEFAULT: 300
• --d-min D_MIN — minimum fragment size in basepair. Any predicted fragment size less than this will be excluded 🚫. DEFAULT: 20
• -m MFOLD MFOLD, --mfold MFOLD MFOLD — selects the regions within MFOLD range of highconfidence enrichment ratio against background to build the model. Fold-enrichment in regions must be lower than the upper limit, and higher than the lower limit. Use it like -m 10 30. DEFAULT: 5 50
• --outdir OUTDIR — if specified, all output files will be written to that directory 📁. Default: the current working directory
• --rfile RFILE — PREFIX of filename of R script for drawing the X-correlation figure 📈. DEFAULT: 'predictd' and the R file will be predicted_model.R
• --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 — sets the verbose level of runtime message 🗣️. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. DEFAULT: 2

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and that's the whole page, you ate that 🍓✨ ngl it's giving "I read the manpage and now I understand my data." iykyk 💜

signing off from macs2 predictd version 2.2.7.1, dated April 2022, in the MACS2_PREDICTD(1) manual — love u bestie, go build that shifting model 🌈💖🦋