Expression analysis

# Creating index
kallisto index -i transcripts.idx transcripts.fasta.gz

# Counting
kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz

References

Manual

https://pachterlab.github.io/kallisto/starting

Github

https://github.com/pachterlab/kallisto

Paper

https://arxiv.org/abs/1505.02710