SALMON_QUANT(1)

✨ SALMON_QUANT(1) ✨

okay bestie, welcome to salmon_quant — the manual page, girl edition 💅

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🌸 NAME 🌸

salmon_quant — highly-accurate, transcript-level quantification estimates straight from your RNA-seq data 🧬✨ like it literally pulls the numbers out of your reads, no cap.

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🦋 DESCRIPTION 🦋

okay so first things first: salmon v1.10.3 🎀 that's the version, write it down, iykyk.

So salmon quant is lowkey a two-for-one situation, it has two modes 👑:

1. one mode quantifies expression using raw reads 🍓
2. and the other one uses already-aligned reads — and those have to be in BAM/SAM format, periodt.

Which algorithm actually gets used? It literally depends on the arguments you pass to salmon quant. The way that works is:

• if you hand salmon some alignments with -a [ --alignments ] → boom, the alignment-based algorithm is the one running 🏃♀️
• otherwise (no -a, no --alignments) → it's the raw-read quantification algorithm for you, bestie 🌈

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🙈 wanna see the help tho?

To view the help for salmon's selective-alignment-based mode, use the command:

salmon quant --help-reads

To view the help for salmon's alignment-based mode, use the command:

salmon quant --help-alignment

fr fr, read the help for whichever mode you're actually using, don't just vibe-check it and hope 💀

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okay that's the whole page, you ate that 🫶

this lil slice of manual came from salmon --no-version-check qua... and it's dated February 2026 — iconic, we stan a timestamped queen 👑💖 mwah, go quantify something ✨