.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH SALMON_QUANT "1" "March 2024" "salmon --no-version-check quant 1.10.2+ds1" "User Commands"
.SH NAME
salmon_quant \- highly-accurate, transcript-level quantification estimates from RNA-seq data 
.SH DESCRIPTION
.IP
salmon v1.10.2
===============
.IP
salmon quant has two modes \fB\-\-\-\fR 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 [ \fB\-\-alignments\fR ]' then the
alignment\-based algorithm will be used, otherwise the algorithm for
quantifying from raw reads will be used.
.IP
to view the help for salmon's selective\-alignment\-based mode, use the command
.IP
salmon quant \fB\-\-help\-reads\fR
.IP
To view the help for salmon's alignment\-based mode, use the command
.IP
salmon quant \fB\-\-help\-alignment\fR