chipextract(1)

💖 chipextract — the Feature Correlation and Extraction Tool 💖

okay bestie, welcome to chipextract, the ChIP-seq tool that's giving matchmaker energy for your genomic features 🧬✨ it's a User Manuals situation and honestly? iconic.

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✨ NAME ✨

chipextract — Feature Correlation and Extraction Tool for ChIP-seq data analysis 🎀

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🌸 SYNOPSIS 🌸

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

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🦋 DESCRIPTION 🦋

so here's the vibe 💅 chipextract reads a ChIP-seq data file (or it'll take it from stdin with [<], she's flexible like that) in SGA format (<SGA file>). That file has two features in it — a reference feature (<feature A>) and a target feature (<feature B>) — and it:

• correlates the genomic tag count distributions for those two features, and
• for each reference feature, extracts the target feature tags that fall into a distance range ([from,to]) relative to the reference feature. periodt.

If you launch chipextract with no arguments at all, it just prints the options list along with their default values. no drama, just receipts 📋

The feature specification must have this exact format:

<feature> = <name> [<+|-|0[strandless]|a[any]|o[oriented]>]

Accepted strand values are the following:

+|-|0[strandless]|a[any]|o[oriented]

If you don't specify a strand, it defaults to a[any]. no cap. 🙈

The <feature> parameter is a name that corresponds to the second field of the SGA file. 🫶

⚠️ bestie listen — the SGA input file MUST BE sorted by sequence name (or chromosome id), position, and strand. like, this is not optional, this is the law 💀

You should check your input SGA file with this command before you do anything:

sort -s -c -k1,1 -k3,3n -k4,4 <SGA file>

The output is a table in text format — and it's lowkey gorgeous ✨ — consisting of all reference features (those are your rows) with relative target tag counts in bins of a given size defined by <window> width (those are your columns). 🌈

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💅 OPTIONS 💅

• -A <ref feature> — the feature that's taken as a reference for correlating chIP-seq tag distances. she's the main character 👑 This parameter is mandatory.
• -B <tar feature> — tags corresponding to the target feature get positionally correlated to tags corresponding to the reference feature. the pairing 🥺 This parameter is mandatory.
• -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, other end: <to> indicates the end. 🎯
• -c <cut-off> — you can optionally drop a value here as a cut-off for the target feature counts. This parameter is optional, and its default value is 1.
• -d — show debug info. the program also performs the sorting order check of the input data file. 🕵️‍♀️
• -h — show the usage message. your help button 🫶
• -w — this one indicates the histogram step size (in bp) or bin. 📊

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🔥 SEE ALSO 🔥

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

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and that's the whole page bestie, you ate that 🍓💜 this little baddie came to you from Bioinformatics, dated July 2015 — yeah she's vintage, she's still slaying, we love her for it. mwah 💋✨