chipcor(1)

📦 version 1.5.5, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 chipcor(1) — the Feature Correlation Tool for ChIP-seq data analysis 💖

okay bestie, sit down, hydrate, because we're about to talk about chipcor, and she is that girl. this is the manual page for the chipcor command from the User Manuals, and we're gonna go through it top to bottom, no skips, no cap. 🎀

✨ NAME ✨

chipcor — Feature Correlation Tool for ChIP-seq data analysis. she correlates features. she makes histograms. she slays. 💅

🌸 SYNOPSIS 🌸

chipcor [ options ] -A <ref feature> -B <tar feature> -b <from> -e <to>
-w <window> [ < ] [ SGA file ]

like, that's the whole vibe right there. options, a reference feature, a target feature, a range, a window, and optionally reading from stdin or a file. periodt. 🦋

🧚 DESCRIPTION 🧚

so here's the tea ☕: chipcor reads a ChIP-seq data file in SGA format — either from a file you pass as <SGA file>, or straight from stdin using [<] — and then it generates histograms showing the positional relationship between two features: a reference feature (<feature A>) and a target feature (<feature B>). it's giving matchmaker but for genomic tags. 💖

and listen — if you just launch chipcor with no arguments at all, it will print the options list for you, along with all their default values. so it's not gonna be mysterious about it, she's an open book. 📖✨

now, the feature specification. it MUST have this exact format:

<feature> = <name> [<+|->]

and the strand spec (+|−) is optional, so you can leave it off if you're not feeling it. no pressure. 🙈

the <feature> parameter is a name that corresponds to the second field of the SGA file. and if you give no feature at all, then all input tags get processed. generous queen. 👑

⚠️ OKAY THIS PART IS IMPORTANT, GIRLIE ⚠️ The SGA input file MUST BE sorted by sequence name (or chromosome id), position, and strand. that's not optional, that's not a suggestion, that's the law. 💀 so please, check your input SGA file with this exact command before you come crying to her: text sort -s -c -k1,1 -k3,3n -k4,4 <SGA file>

like literally just run that. it's free. it's fast. it will save your whole life. 🫶

💅 OPTIONS 💅

  • -A <ref feature> — the feature that's taken as the reference for correlating chIP-seq tag distances. this one is mandatory, bestie. no -A, no service. 🚫
  • -B <tar feature> — the tags that correspond to the target feature get positionally correlated to the tags of the reference feature. also mandatory. both of them. always. 💯
  • -b <from> — the relative distance between the two features is analysed within a given range, and <from> is where that range begins. 🌱
  • -e <to> — same range situation, but <to> is where it ends. 🏁
  • -c <cut-off> — you can optionally drop a value here as a cut-off for the input tag counts. this parameter is optional, and its default value is 1. so chill, you don't have to set it. 🌈
  • -d — show debug info. with this on, the program performs the sorting order check of the input data file. lowkey your bestie for catching a badly sorted file. 🔍
  • -h — show the usage message. the classic. the icon. the "help me please" button. 🆘
  • -w — this indicates the histogram step size (in bp). yeah she takes no argument in this listing, that's just how the page tells it. 📏
  • -n <norm> — histogram normalization. this is the big one, so let's break it all the way down:
    • norm = 0 — Raw counts. histogram bin entries display the product between reference and target counts at the corresponding relative distance. that's the default, btw. 🍼
    • norm = 1 — Count density. histogram entries are normalized by the total number of reference counts and the window width. so the measurement becomes a target count density (per length unit and reference count unit). ✨
    • norm = 2 — Global Normalization. histogram entries are normalized by the total number of reference and target counts, plus the window width. and heads up: the curve should approach one for large correlation distances (or weak correlation). 🫧

the default value is 0. 📌

  • -o — the Oriented strand option. requiring oriented strand processing means reverting the chromosome axis when the reference feature is on the - strand. she flips the whole axis, dramatic and correct. 🔄💅

👑 SEE ALSO 👑

go read these too, they're all in the same friend group:

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

and that's the whole page, bestie. you ate. 💖✨

signed off with love from the Bioinformatics girlies — this one's from July 2015, and that's the version we're all living in. mwah. 🎀🦋💜

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