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SALMON_QUANT(1) |
User Commands |
SALMON_QUANT(1) |
NAME¶
salmon_quant - highly-accurate, transcript-level quantification estimates from
RNA-seq data
DESCRIPTION¶
- Salmon v0.7.2 ===============
- 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