chipcenter(1)

💖 chipcenter(1) 💖

User Manuals ✨ the ChIP-seq girlies' favorite centering tool 🎀

🌸 NAME 🌸

chipcenter — the Feature Centering Tool for ChIP-seq data analysis, bestie 💅

🦋 SYNOPSIS 🦋

chipcenter [ options ] [ -f <feature name> ] -s <shift> [ < ] [ SGA file ]

✨ DESCRIPTION ✨

okay so chipcenter reads a ChIP-seq data file (or it'll take it straight from stdin with [<]) in SGA format (<SGA file>), and it shifts — by <shift> — the ChIP-tag positions that correspond to a specific feature (<feature name>) over to the estimated center-positions of DNA fragments. iconic behavior, no notes 💅

If you don't set a feature specification, the program just accepts all oriented lines of the input SGA. Strandless features get ignored, periodt. And if you specify -r <new feature>, the feature field gets replaced with that <new feature> string. glow-up for your feature names fr fr ✨

ngl, launching chipcenter with zero arguments will print the options list, along with all their default values. so if you're ever lost, just run it bare and it'll tell you everything 🫶

The <feature> parameter is a name that matches up with the second field of the SGA file. It might optionally include the strand specification (+|-). And if no feature is given, then literally all input tags get processed. simple as that 💖

👑 OPTIONS 👑

• -c <cut-off> — you can drop a value here as a cut-off for the input tag counts. it's optional, and its default value is 1. 🍓
• -d — show debug info. 👀
• -f <feature name> — this one is for selecting all or a sub-set of chIP-seq input tags. the feature name lives in the second field of the SGA-formatted input file. if you don't give a feature name, then all features get selected. 🎀
• -h — show the usage message. the classic cry for help button 🫶
• -r <new feature> — defines a new feature name for feature replacement. ✨
• -s <shift> — defines the relative shift (in bp) of observed ChIP-tags over to the estimated center-positions of DNA fragments. > ⚠️ this parameter is mandatory. you can't skip it, bestie, it's the whole point of the program 😭
• -z — set the (output) strand to zero. optional, but slay. 💅

🌈 SEE ALSO 🌈

chipcor(1), chipextract(1), chippeak(1) chippart(1) chipscore(1),

okay that's the whole page!! this one comes to you from Bioinformatics, dated July 2015 — an absolute vintage era for the pipeline, and it still ate 💖✨ mwah, go center those fragments bestie 🦋🌸