chipscore(1)

💖 chipscore(1) 💖

okay bestie, sit down, grab your boba, because we're about to talk about chipscore — it lives in the User Manuals section and it is genuinely iconic for ChIP-seq girlies. no cap. 🧬✨

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🌸 NAME 🌸

chipcor — Feature Extraction Tool for ChIP-seq data analysis 🦋

(and yes, that's literally what it says, we don't make the rules, we just report them 💅)

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✨ SYNOPSIS ✨

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

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🎀 DESCRIPTION 🎀

so like, chipscore reads a ChIP-seq data file (or it reads from stdin, that's the [<] vibe) in SGA format (<SGA file>), and then it compares two features — a reference feature (<feature A>) and a target feature (<feature B>) — all about where they sit relative to each other. then it extracts feature A tags that are enriched in feature B tags, according to a given Count Output Threshold or Score (-t). slay. 🔥

if you launch chipscore with zero arguments, it just prints the options list, along with all their default values. very "here's the menu, bestie" of it. 🫶

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🦋 the feature specification 🦋

the feature spec MUST have this exact format:

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

the strand specification (+|) — wait, the strand spec is + or - — is optional. 💜

the <feature> parameter is a name that corresponds to the second field of the SGA file. and if you don't give any feature at all? then all input tags get processed. generosity, we love to see it. 🌈

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💀 the sort check (do NOT skip this) 💀

the SGA input file MUST BE sorted by sequence name (or chromosome id), position, and strand. like, this is not a suggestion, this is the law. 😭

you should check your input SGA file with this command, fr fr:

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

bestie. run the check. don't be the person whose tags are out of order. the program will not hold your hand about this. 🙈

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💅 OPTIONS 💅

• -A <ref feature> — the feature that's taken as a reference for correlating chIP-seq tag distances. 🎀

this parameter is mandatory. you cannot skip it, periodt.

• -B <tar feature> — tags corresponding to the target feature get positionally correlated to the tags corresponding to the reference feature. ✨

this one is mandatory too. both of them. always. 👑

• -b <from> — the relative distance between the two features gets analysed within a given range, and <from> is where that range begins. 🌱
• -e <to> — same deal, same range, 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 10. 🍓
• -d — show debug info. and when you do, the program performs the sorting order check of the input data file. it's giving "I'm watching you" energy. 👀
• -h — show the usage message. the classic. the icon. the "help me please" button. 💖
• -o — Oriented strand option. requiring oriented strand processing means reverting the chromosome axis when the reference feature is on the - strand. yes, we're flipping the whole axis, no cap. 🔄
• -r — Reverse extraction process. the program extracts sites that are depleted in feature B. opposite day, but make it science. 🌀
• -q — report feature B tag counts as 'feature_name=<int>'. cute little reporting moment. 📝
• -t <thres> — Output threshold or score. the program extracts feature A tags that are enriched in feature B tags according to a given count output threshold. the default value is 0. ⭐

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🌈 SEE ALSO 🌈

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

go read those too, they're the friend group, they come as a set. 🫶🦋

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and that's the whole page, bestie!! 💜 this one came from the Bioinformatics corner of the world, dated June 2015 — so like, vintage, but make it genomics. mwah, go sort your SGA file. 😘✨