Expression analysis

# Creating index
salmon index -t transcripts.fa -i transcripts_index --type quasi -k 31

# Counting
salmon quant -i index -l IU -1 read1.fq -2 read2.fq -o out

References

Manual

http://salmon.readthedocs.io/en/latest/salmon.html

Github

https://github.com/COMBINE-lab/salmon

Paper

http://biorxiv.org/content/early/2015/06/27/021592