DESCRIPTION

Salmon v0.4.2 ===============

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 alignment-based mode, use the command

salmon quant --help-alignment

to view the help for salmon's read-based mode, use the command

salmon quant --help-reads