Salmon quantifies transcript abundance from RNA-seq reads using lightweight selective alignment against a transcriptome, correcting for GC and sequence-specific biases.
Example
1salmon index -t transcripts.fa -i salmon_index2salmon quant -i salmon_index -l A -1 r1.fq -2 r2.fq -p 8 -o quant
Outputs integrate cleanly with tximport and downstream differential-expression tools.
