DOKK / manpages / debian 11 / salmon / salmon-quant.1.en
SALMON_QUANT(1) User Commands SALMON_QUANT(1)

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

salmon v1.4.0 ===============
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.
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
June 2021 salmon --no-version-check quant 1.4.0+ds1