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Code Block
titleTophat commands
nano commands.tophat
tophat -p 2 -r 200 -G reference/genes.gtf -o C1_R1_thout reference/genome.fa data/GSM794483_C1_R1_1.fq data/GSM794483_C1_R1_2.fq
tophat -p 2 -r 200 -G reference/genes.gtf -o C1_R2_thout reference/genome.fa data/GSM794484_C1_R2_1.fq data/GSM794484_C1_R2_2.fq
tophat -p 2 -r 200 -G reference/genes.gtf -o C1_R3_thout reference/genome.fa data/GSM794485_C1_R3_1.fq data/GSM794485_C1_R3_2.fq
tophat -p 2 -r 200 -G reference/genes.gtf -o C2_R1_thout reference/genome.fa data/GSM794486_C2_R1_1.fq data/GSM794486_C2_R1_2.fq
tophat -p 2 -r 200 -G reference/genes.gtf -o C2_R2_thout reference/genome.fa data/GSM794487_C2_R2_1.fq data/GSM794487_C2_R2_2.fq
tophat -p 2 -r 200 -G reference/genes.gtf -o C2_R3_thout reference/genome.fa data/GSM794488_C2_R3_1.fq data/GSM794488_C2_R3_2.fq

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