SALMON_QUANT(1)

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

DESCRIPTION

    salmon v1.10.3 ===============

    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