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/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --no-novel-juncs --bowtie1 -p 8 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o SRR870466-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final SRR870466_1.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --no-novel-juncs --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 SRR870467-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final SRR870467_1.fastq.gz SRR870467_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/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --no-novel-juncs --bowtie1 -p 8 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o SRR870507-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final SRR870507_1.fastq.gz SRR870507_2.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --no-novel-juncs --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 SRR870508-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final SRR870508_1.fastq.gz SRR870508_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/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --no-novel-juncs --bowtie1 -p 8 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o SRR870509-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final SRR870509_1.fastq.gz SRR870509_2.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --no-novel-juncs --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 SRR870516-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final SRR870516_1.fastq.gz SRR870516_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/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --no-novel-juncs --bowtie1 -p 8 --no-discordant --no-mixed --read-edit-dist 4 --read-mismatches 4 --min-intron-length 10 --max-intron-length 1000000 --GTF /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/Smic.genome.annotation.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/transcriptome-indexes/Smic.genome.annotation -o SRR870522-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final SRR870522_1.fastq.gz SRR870522_2.fastq.gz
export PATH=/oak/stanford/groups/akundaje/marinovg/programs/bowtie-0.12.9/:/oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19:/oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/:$PATH; python /oak/stanford/groups/akundaje/marinovg/programs/tophat-2.0.8.Linux_x86_64/tophat --no-novel-juncs --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 SRR870524-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final SRR870524_1.fastq.gz SRR870524_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 --no-novel-juncs --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 SRR870525-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.scaffold.final SRR870525_1.fastq.gz SRR870525_2.fastq.gz