zcat aiptasia_genome.scaffolds.25mers.fa.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -p 8 -v 0 --k 2 -m 1 -t --best --strata -f --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - aiptasia_genome.scaffolds.25mers.unique
zcat aiptasia_genome.scaffolds.36mers.fa.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -p 8 -v 0 --k 2 -m 1 -t --best --strata -f --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - aiptasia_genome.scaffolds.36mers.unique
zcat aiptasia_genome.scaffolds.50mers.fa.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -p 8 -v 0 --k 2 -m 1 -t --best --strata -f --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - aiptasia_genome.scaffolds.50mers.unique
zcat aiptasia_genome.scaffolds.75mers.fa.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -p 8 -v 0 --k 2 -m 1 -t --best --strata -f --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - aiptasia_genome.scaffolds.75mers.unique
zcat aiptasia_genome.scaffolds.100mers.fa.gz | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds -p 8 -v 0 --k 2 -m 1 -t --best --strata -f --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools sort - aiptasia_genome.scaffolds.100mers.unique