export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/aiptasia_genome.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/transcriptome-indexes/aiptasia_genome -o Aiptasia-CC7-Endo-Heat-Light-0hrs-b-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0 /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds  CEHL_TM0b.36mers.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/aiptasia_genome.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/transcriptome-indexes/aiptasia_genome -o Aiptasia-CC7-Endo-Heat-Light-0hrs-c-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0 /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds  CEHL_TM0c.36mers.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/aiptasia_genome.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/transcriptome-indexes/aiptasia_genome -o Aiptasia-CC7-Endo-Heat-Light-0hrs-d-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0 /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds  CEHL_TM0d.36mers.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/aiptasia_genome.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/transcriptome-indexes/aiptasia_genome -o Aiptasia-CC7-Endo-Heat-Light-0hrs-e-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0 /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds  CEHL_TM0e.36mers.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/aiptasia_genome.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/transcriptome-indexes/aiptasia_genome -o Aiptasia-CC7-Endo-Heat-Light-0hrs-f-1x36mers-TopHat-2.0.8-Aiptasia_pallida-1.0 /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Cnidaria/Aiptasia_pallida-1.0/bowtie-indexes/aiptasia_genome.scaffolds  CEHL_TM0f.36mers.fastq.gz