/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat -p 2 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --no-novel-juncs --output-dir tophat_GZS-17_R1 --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/Mus_musculus/UCSC/mm9/mRNA/transcripts /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome 131218_SND393_A_L006_GZS-17_R1.trm.fq.gz