cd /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes; /oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/bowtie-build -f aiptasia_genome.scaffolds.fa aiptasia_genome.scaffolds