---
name: "salmon-quant"
section: "1"
platform: "linux"
package: "salmon"
version: "1.10.2+ds1-1+b5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/salmon-quant"
---

# salmon-quant(1)

highly-accurate, transcript-level quantification estimates from RNA-seq data

## NAME

salmon\_quant - highly-accurate, transcript-level quantification estimates from RNA-seq data

## DESCRIPTION

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  salmon v1.10.2 ===============

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  salmon quant has two modes **---** one quantifies expression using raw reads and the other makes use of already-aligned reads (in BAM/SAM format). Which algorithm is used depends on the arguments passed to salmon quant. If you provide salmon with alignments '-a \[ **--alignments** \]' then the alignment-based algorithm will be used, otherwise the algorithm for quantifying from raw reads will be used.

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

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  salmon quant **--help-reads**

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

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  salmon quant **--help-alignment**