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/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o smic_nn_R3-SRR3337494-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final smic_nn_R3-SRR3337494_1.fastq.gz smic_nn_R3-SRR3337494_2.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o smic_DS_R1-SRR3337495-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final smic_DS_R1-SRR3337495_1.fastq.gz smic_DS_R1-SRR3337495_2.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/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o smic_DS_R2-SRR3337496-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final smic_DS_R2-SRR3337496_1.fastq.gz smic_DS_R2-SRR3337496_2.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o smic_DS_R3-SRR3337497-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final smic_DS_R3-SRR3337497_1.fastq.gz smic_DS_R3-SRR3337497_2.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/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o smic_nn_R1-SRR3337498-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final smic_nn_R1-SRR3337498_1.fastq.gz smic_nn_R1-SRR3337498_2.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o smic_16C_R1-SRR3337500-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final smic_16C_R1-SRR3337500_1.fastq.gz smic_16C_R1-SRR3337500_2.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/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o smic_16C_R2-SRR3337501-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final smic_16C_R2-SRR3337501_1.fastq.gz smic_16C_R2-SRR3337501_2.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o smic_16C_R3-SRR3337502-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final smic_16C_R3-SRR3337502_1.fastq.gz smic_16C_R3-SRR3337502_2.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/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o smic_36C_R1-SRR3337503-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final smic_36C_R1-SRR3337503_1.fastq.gz smic_36C_R1-SRR3337503_2.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -p 8 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o smic_36C_R2-SRR3337504-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final smic_36C_R2-SRR3337504_1.fastq.gz smic_36C_R2-SRR3337504_2.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 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o smic_36C_R3-SRR3337505-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final smic_36C_R3-SRR3337505_1.fastq.gz smic_36C_R3-SRR3337505_2.fastq.gz