/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --GTF ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.gtf --output-dir Diamide_0min.2x50mers.TopHat-2.0.8/Cufflinks-2.0.2-SacCer_Apr2011.20 Diamide_0min.2x50mers.TopHat-2.0.8/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --GTF ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.gtf --output-dir Diamide_15min.2x50mers.TopHat-2.0.8/Cufflinks-2.0.2-SacCer_Apr2011.20 Diamide_15min.2x50mers.TopHat-2.0.8/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --GTF ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.gtf --output-dir Diamide_30min.2x50mers.TopHat-2.0.8/Cufflinks-2.0.2-SacCer_Apr2011.20 Diamide_30min.2x50mers.TopHat-2.0.8/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --GTF ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.gtf --output-dir Diamide_45min.2x50mers.TopHat-2.0.8/Cufflinks-2.0.2-SacCer_Apr2011.20 Diamide_45min.2x50mers.TopHat-2.0.8/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --GTF ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.gtf --output-dir Diamide_60min.2x50mers.TopHat-2.0.8/Cufflinks-2.0.2-SacCer_Apr2011.20 Diamide_60min.2x50mers.TopHat-2.0.8/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --GTF ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.gtf --output-dir Diamide_Hsf_0min.2x50mers.TopHat-2.0.8/Cufflinks-2.0.2-SacCer_Apr2011.20 Diamide_Hsf_0min.2x50mers.TopHat-2.0.8/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --GTF ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.gtf --output-dir Diamide_Hsf_30min.2x50mers.TopHat-2.0.8/Cufflinks-2.0.2-SacCer_Apr2011.20 Diamide_Hsf_30min.2x50mers.TopHat-2.0.8/accepted_hits.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 8 --GTF ~/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.gtf --output-dir Diamide_Hsf_60min.2x50mers.TopHat-2.0.8/Cufflinks-2.0.2-SacCer_Apr2011.20 Diamide_Hsf_60min.2x50mers.TopHat-2.0.8/accepted_hits.bam