salmon_quant - highly-accurate, transcript-level quantification
estimates from RNA-seq data
- salmon v1.4.0 ===============
- 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 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