MACS2_BDGCMP(1)

💖 NAME 💖

macs2_bdgcmp — Model-based Analysis for ChIP-Sequencing ✨ (yes bestie, that's the whole name, it's giving very "the acronym ate and left no crumbs")

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🎀 DESCRIPTION 🎀

okay so here's the whole vibe of how you call it, verbatim, no notes:

usage: macs2 bdgcmp [-h] -t TFILE -c CFILE [-S SFACTOR] [-p PSEUDOCOUNT]
       [-m {ppois,qpois,subtract,logFE,FE,logLR,slogLR,max}
       [{ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} ...]]
              [--outdir OUTDIR] (--o-prefix OPREFIX | -o OFILE [OFILE ...])

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✨ options ✨

• -h, --help — shows this help message and then dips. that's it, that's the whole job 💅
• -t TFILE, --tfile TFILE — the Treatment bedGraph file, like *_treat_pileup.bdg from MACSv2. REQUIRED — you literally cannot skip this one, it's the main character 🫶
• -c CFILE, --cfile CFILE — the Control bedGraph file, like *_control_lambda.bdg from MACSv2. REQUIRED — also non-negotiable, no skipping ✋
• -S SFACTOR, --scaling-factor SFACTOR — scaling factor for the treatment and control tracks. fr fr, keep it at 1.0 or just leave it default in most cases. Only set it if you have SPMR output from MACS2 callpeak and you're planning to calculate scores the same way the MACS2 callpeak module does. If you wanna simulate 'callpeak' without '--to-large', calculate the effective smaller sample size after filtering redundant reads in millions (so like, if effective reads are 31,415,926 you'd put 31.415926) and feed that into '-S'. For 'callpeak --to-large', calculate the effective reads using the larger sample instead. DEFAULT: 1.0 🌸
• -p PSEUDOCOUNT, --pseudocount PSEUDOCOUNT — the pseudocount used for calculating logLR, logFE or FE. It gets applied after the normalization of sequencing depth, so don't come for me about order. DEFAULT: 0.0, no pseudocount is applied. 🍓
• -m {ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} [{ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} ...], --method {ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} [{ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} ...] — the method you use while calculating a score in any bin by comparing the treatment value and the control value. Available choices are: ppois, qpois, subtract, logFE, logLR, and slogLR. Here's what they actually mean, bestie:
  • ppois = Poisson Pvalue (in -log10(pvalue) form) using control as lambda and treatment as observation
  • qpois = q-value through a BH process for poisson pvalues
  • subtract = subtraction from treatment
  • logFE = linear scale fold enrichment
  • FE = log10 fold enrichment (you need to set pseudocount for this one)
  • logLR = log10 likelihood between ChIP-enriched model and open chromatin model (also needs pseudocount set)
  • slogLR = symmetric log10 likelihood between two ChIP-enrichment models
  • max = maximum value between the two tracks

Default option is ppois. 👑

• --outdir OUTDIR — if you specify it, all output files get written to that directory instead. Default: the current working directory 📁
• --o-prefix OPREFIX — the PREFIX of the output bedGraph file where the scores get written. If you give it as A and the method is 'ppois', the output file will be A_ppois.bdg. Mutually exclusive with -o/--ofile — pick a lane, you can't have both 🚫
• -o OFILE [OFILE ...], --ofile OFILE [OFILE ...] — output filename. Mutually exclusive with --o-prefix. And listen: the number and the order of arguments for --ofile must be exactly the same as for -m. Match them up, don't freestyle 🙈

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quick vibe check: --o-prefix and -o/--ofile are mutually exclusive, so don't try to run both at once, it's not that kind of party.

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and that's the whole page, bestie!! 🦋 this was macs2 bdgcmp 2.2.7.1, dated April 2022, from the MACS2_BDGCMP(1) manual — go calculate some scores, you're gonna slay 💖✨👑