/data/results/tools/align/tophat-2.0.12.Linux_x86_64/tophat -p 3 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --no-novel-juncs --output-dir tophat_015 --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 R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GSkP4-Ab42Lib.IonXpressRNA_015.fastq