chippeak(1)

💖 chippeak — the manual, but make it make sense 💖

okay bestie, buckle up, because chippeak is genuinely that girl. she lives in the User Manuals section of the manual, and she is here to find your signal peaks. let's go 🦋

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✨ NAME ✨

chippeak — locates signal peaks within a set of tag positions produced by a ChIP-Seq experiment. yes that's the whole job. she finds the peaks. she ate. 💅

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🌸 SYNOPSIS 🌸

chippeak [ options ] [ -f <feature name> ] -t <threshold> -w <window> -v
<vicinity> [ < ] [ SGA file ]

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🎀 DESCRIPTION 🎀

so here's the vibe: chippeak reads a ChIP-seq data file in SGA format — either from a file (<SGA file>) or straight from stdin (<) — and it detects signal peaks for ChIP-tag positions that correspond to a specific feature <feature name>, whenever you actually give it one. no feature? no problem. then it just processes all the input tags. all of them. every single one. periodt. 👑

if you launch chippeak with zero arguments, it'll print the options list for you, along with all their default values. it's giving helpful. it's giving "here's the menu, bestie." 🫶

the <feature> parameter is a name that matches the second field of the SGA file. it can optionally include the strand specification (+|-). and again, fr fr: if no feature is given, then all input tags are processed. that part matters.

💀 CRITICAL, NO CAP: the SGA input file MUST BE sorted by sequence name (or chromosome id), position, and strand. like, it has to be. do not skip this. do not pass go. check your input SGA file with this exact command first:

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

the output is an SGA-formatted list containing signal peak locations. iconic. that's the whole point of her. ⭐

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💅 OPTIONS 💅

• -c <cut-off> — you can hand her a value to use as a cut-off for the input tag counts. this one's optional, and its default value is 1.
• -d — show debug info. with this on, the program performs the sorting order check of the input data file. basically she double-checks that your file is actually sorted like she asked. 👀
• -f <feature name> — this parameter selects all, or just a sub-set, of the ChIP-seq input tags. the feature name is specified in the second field of the SGA-formatted input file.

if no feature name is given, then all features are selected. (yes, we said it again. it's important.)

• -h — show the usage message. short king of an option, honestly.
• -o — oriented strand processing. if you select this, peaks are separately detected on the plus and minus strands, respectively. separate. not together. 🌈
• -r — Refine Peak Positions. if you select this, a post-processing step turns on to improve peak location. for the initially selected peaks, the position gets recomputed as the center of gravity of the counts in the region defined by the <window> parameter. she's doing math. she's thriving. 🧚
• -t <threshold> — Peak Threshold. the cumulative tag count within a range w should be bigger than or equal to Threshold t. the default value is 50.

this parameter is optional.

• -v <vicinity> — this defines the minimal distance (in bp) amongst a group of local maxima (aka high count values).

🚨 this parameter is mandatory. no vibe-checking your way out of it.

• -w <window> — this defines the integration range (in bp) of signal (or tag) counts.

🚨 this parameter is mandatory too. mandatory squared. mandatory with a bow on it. 🎀

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🔥 SEE ALSO 🔥

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

go read those too, bestie, the whole squad is worth your time 💜

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and that's the whole page!! this one came from Bioinformatics, dated July 2015 — so if you're reading this, shoutout to the original authors for handing us the blueprint, and shoutout to you for reading the whole thing. slay, go find some peaks, and remember: sort your file first. mwah 🫶✨