/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --compatible-hits-norm --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/aiptasia_genome.gtf --output-dir Aiptasia-CC7-Endo-Heat-Light-0hrs-a-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/Cufflinks-2.0.2 Aiptasia-CC7-Endo-Heat-Light-0hrs-a-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --compatible-hits-norm --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/aiptasia_genome.gtf --output-dir Aiptasia-CC7-Endo-Heat-Light-0hrs-b-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/Cufflinks-2.0.2 Aiptasia-CC7-Endo-Heat-Light-0hrs-b-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --compatible-hits-norm --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/aiptasia_genome.gtf --output-dir Aiptasia-CC7-Endo-Heat-Light-0hrs-c-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/Cufflinks-2.0.2 Aiptasia-CC7-Endo-Heat-Light-0hrs-c-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --compatible-hits-norm --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/aiptasia_genome.gtf --output-dir Aiptasia-CC7-Endo-Heat-Light-0hrs-d-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/Cufflinks-2.0.2 Aiptasia-CC7-Endo-Heat-Light-0hrs-d-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --compatible-hits-norm --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/aiptasia_genome.gtf --output-dir Aiptasia-CC7-Endo-Heat-Light-0hrs-e-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/Cufflinks-2.0.2 Aiptasia-CC7-Endo-Heat-Light-0hrs-e-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --compatible-hits-norm --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/aiptasia_genome.gtf --output-dir Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/Cufflinks-2.0.2 Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0/accepted_hits.bam