/data/results/tools/align/tophat-1.4.0.Linux_x86_64/tophat -p 10 -n 2 -o wt0hrep1d -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -C /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/0hrep1b.fastq