chippart(1)

💖 chippart(1) — the partitioning tool for ChIP-seq data analysis 💖

okay bestie, gather round 🫶 this is the manual page for chippart, living in the User Manuals section of your friendly neighbourhood man pages. She partitions. She slays. Let's go. ✨

🌸 NAME 🌸

chippart — Partitioning Tool for ChIP-seq data analysis 👑

✨ SYNOPSIS ✨

chippart [ options ] -f <feature name> -p <transition penalty> -s
<density threshold> [ < ] [ SGA file ]

🦋 DESCRIPTION 🦋

So like, chippart reads a ChIP-seq data file — or it'll take it straight from stdin with [<], no big deal — in SGA format (<SGA file>), and then it goes and finds signal-enriched regions across the whole file for ChIP-tag positions that correspond to a specific feature <feature name>, or honestly, all features if you want the full menu. 💅

Launch chippart with zero arguments and it'll just print the options list, defaults included. Iconic behaviour, honestly. It's giving "here's the menu, order whenever." 🎀

The <feature> parameter is a name that matches the second field of the SGA file. It can optionally include the strand spec (+|-) too. And if you don't give a feature at all? Then every single input tag gets processed. Main character energy: all tags invited to the party. 🌈

⚠️ OKAY THIS PART MATTERS, FR FR: the SGA input file MUST BE sorted by sequence name (or chromosome id), position, and strand. No cap. You should check your input SGA file with this exact command before you do anything else:

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

The output is an SGA-formatted list containing the regions of interest. 🎉

The program also generates a statistical report to stderr with all of this tea:

• Total number of processed sequences, total DNA length, and total number of fragments;
• Total length of fragments, average fragment length, and percentage of total DNA length;
• Percentage of total counts, average number of counts, and number of count per bp (count density).

Numbers! Stats! We love a data girlie. 📊💖

💅 OPTIONS 💅

• -c <cut-off> — you can drop a value here to set a cut-off for the input tag counts. This one's optional, bestie — its default value is 1.
• -d — show debug info. The program does the sorting order check of the input data file. 🕵️‍♀️ Useful when you're like "why is this file sus"
• -f <feature name> — this parameter selects all or a sub-set of ChIP-seq input tags. The feature name is specified in the second field of the SGA-formatted input file. And if you don't give a feature name? Then all features are selected. The more the merrier. 🫶
• -h — show the usage message. Your little cry-for-help button, and we've all been there. 😭
• -p <transition penalty> — assigns a (negative) score to a transition between signal-enriched and signal-poor regions. This parameter needs to be negative. It therefore controls the fragment length — i.e. high penalty → long fragments. 🦋 This parameter is mandatory.
• -s <density threshold> — a region must have a count density higher than the value specified by the <density threshold> in order to be considered a signal-enriched DNA stretch. Also mandatory, so don't forget her. 💀

👑 SEE ALSO 👑

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

okay that's the whole page, you ate it, periodt 🎀 this one's from Bioinformatics, dated July 2015, and it's the chippart(1) page — go partition something gorgeous bestie, iykyk 💖✨🌸🦋