NAME

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

DESCRIPTION

              salmon v0.12.0 ===============

              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 quasi-mapping-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