JOINGENES(1)

✨ JOINGENES ✨ (like, the joingenes(1) manual page bestie 💖)

okay so. you found the manual page for joingenes, and honestly? it's giving "quiet little program that does SO much". no cap.

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🌸 NAME 🌸

joingenes — merge several gene sets into one 🧬💅

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🎀 SYNOPSIS 🎀

joingenes [parameters] --genesets=file1,file2,...  --output=ofile

that's the whole vibe. you give it parameters, you give it genesets, you give it an output file. periodt.

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🦋 DESCRIPTION 🦋

so this program works in several steps, and we're gonna walk through every single one because that's the whole point of a manpage, bestie:

1. divide the set of all transcripts into smaller sets, in which all transcripts are on the same sequence and are overlapping at least with one other transcript in this set (this kind of set is called an "overlap").
2. delete all duplications of transcripts and save the variant with the highest "score". bye bye dupes 👋
3. if sequence ranges are set for some transcripts, the program detects whether the distance to that range is dangerously close. yes, it's doing a vibe check on your ranges.
4. join, which is the main character of this whole operation:
   • if there is a transcript dangerously close to one/both end(s) of a sequence range, the program creates a copy without the corresponding terminal exon.
   • if there is a transcript with start or stop codon in a set and a second one without this codon and they are "joinable", then this step joins the corresponding terminal exons.
5. selection: selects the "best" gene structure out of all possible "maximum" gene structures.
   • a "maximum" gene structure is a set of transcripts from an overlap so that there is no other transcript in the overlap which can be added to the set without producing a "contradiction".
   • a gene structure is "better" than another one if it has the transcript with the highest "score", which is not present in the other gene structure.

like. the algorithm has tastes. it has opinions. and it WILL pick the best one. slay 🔥

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💅 OPTIONS 💅

✨ Mandatory parameters (you literally cannot skip these, bestie) ✨

• --genesets=file1,file2,.../-g file1,file2,... — where file1,file2,...,filen have to be data files with genesets in GTF format. yes, GTF. not GFF. don't do that to yourself.
• --output=ofile/-o ofile — where ofile is the name for an output file (GTF).

🌈 Optional parameters (the fun lil extras) 🌈

• --priorities=pr1,pr2,.../-p pr1,pr2,... — where pr1,pr2,...,prn have to be positiv integers (different from 0). Have to be as many as filenames are added. Bigger numbers means a higher priority. If no priorities are added, the program will set all priorties to 1. This option is only useful if there is more than one geneset. If there is a conflict between two transcripts, so that they can not be picked in the same genestructure, joingenes decides for the one with the highest priority. it's a popularity contest but make it genomics 👑
• --errordistance=x/-e x — where x is a non-negative integer. If a prediction is ⇐x bases next to a prediction range border, the program supposes that there could be a mistake. Default is 1000. To disable the function, set errordistance to a negative number (e.g. -1). it's the "hmm that's SUS" radius.
• --genemodel=x/-m x — where x is a genemodel from the set {eukaryote, bacterium}. Default is eukaryotic. pick your fighter 💖
• --alternatives/-a — If this flag is set, the program joins different genes if the transcripts of the genes are alternative variants.
• --suppress=pr1,pr2,../-s pr1,pr2,... — where pr1,pr2,...,prm have to be positive integers (different from 0). Default is none. If the core of a joined/non-joined transcript has one of these priorities it will not occur in the output file. ghosting, but for transcripts 👻
• --stopincoding/-i — If this flag is set, the program joins the stop_codons to the CDS.
• --nojoin/-j — If this flag is set, the program will not join/merge/shuffle; it will only decide between the unchanged input transcripts and output them. it's the "no thoughts, head empty, just vibes" mode 😌
• --noselection/-l — If this flag is set, the program will NOT select at the end between "contradictory" transcripts. "contradictory" is self defined with respect to known biological terms. The selection works with a self defined scoring function.
• --onlycompare/-c — If this flag is set, it disables the normal function of the program and activates a compare and separate mode to separate equal transcripts from non equal ones. side quest activated 🧚

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🫶 AUTHORS 🫶

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth. legends, honestly. absolute icons. 💜

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📚 ADDITIONAL DOCUMENTATION 📚

An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz. go read it if you want the FULL lore, no crumbs left behind 🍓

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ngl if you got this far you're already better at Unix than half the internet. go join some genes. you got this 💖

and that's a wrap on the joingenes(1) page from the AUGUSTUS docs — signing off, mwah 💅✨