PROPMAPPED(1)

📦
version 2.0.8 · 2 versions
, in debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ propmapped ✨

okay bestie, sit down, hydrate, because this one is a little baby of a manpage and we're gonna devour it 💅

propmapped is a toolkit for processing next-gen sequencing data. yes, literally that. it's giving "small but mighty" and we love that for it.

🌸 DESCRIPTION 🌸

propMapped v2.0.4 🦋

What does it do? It calculates the proportion of mapped reads/fragments. That's the whole vibe. You feed it mapping results, it tells you what fraction actually mapped. iconic behavior, no notes.

Usage:

./prommapped [options] -i <file>
heads up bestie: the usage line says prommapped, not propmapped. that is exactly how it's written in the original, so I'm keeping it character-for-character. not my typo, not yours to fix. 🫶

🫶 Required arguments 🫶

you literally cannot run this without the following. it will simply not happen. main character requirement energy.

  • -i <string> — the input file, aka the one holding your read mapping results. and guess what? both SAM and BAM formats are supported 😌 so bring whichever one you've got, she's flexible.

🍓 Optional arguments 🍓

these are the little sprinkles on top. use them if you want, skip them if you don't, she's not gonna be dramatic about it.

  • -o <string> — name of the output file, and yes it includes your mapping statistics. your results, your filename, your rules. 💖
  • -f — if you specify this, fragments (read pairs) get counted instead of individual reads. so like, pairs over singles. 💞
tiny lil caveat: this option is only applicable for paired-end reads. don't come for me if you're running single-end and wondering why nothing's cute. 🙈
  • -p — if you specify this, only properly paired reads will be counted. picky? yes. correct? also yes. 💅
same deal here: this one is also only applicable for paired-end reads. no cap.

👑 AUTHOR 👑

this manpage was written by Alexandre Mestiashvili for the Debian distribution, and it can be used for any other usage of the program. so like, it's Debian's but also everyone's. generous queen behavior. 🎀

and that's the whole page, bestie!! go map some reads, calculate some proportions, live your truth 🦋✨

signing off from propmapped 2.0.3, dated March 2023 — mwah, take care of her 💖💅

📦 where this page comes from