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_minutum_Clade_B1_Ver1.120123/symbB.v1.2.augustus.gtf --transcriptome-index /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/transcriptome-indexes/symbB.v1.2.augustus -o SRR870465-TopHat-2.0.8 /oak/stanford/groups/akundaje/marinovg/genomes/Dinoflagellata/Symbiodinium_minutum_Clade_B1_Ver1.120123/bowtie-indexes/symbB.v1.0.genome SRR870465_1.fastq.gz SRR870465_2.fastq.gz