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