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