/woldlab/castor/data00/home/georgi/programs/tophat-2.0.8.Linux_x86_64/tophat --bowtie1 -o test-ce10 -p 16 --no-novel-juncs --transcriptome-index /woldlab/castor/data00/home/georgi/genomes/ce10/bowtie-indexes/Caenorhabditis_elegans.WS220.66 --GTF /woldlab/castor/data00/home/georgi/genomes/ce10/Caenorhabditis_elegans.WS220.66.gtf /woldlab/castor/data00/home/georgi/genomes/ce10/bowtie-indexes/ce10 C.elegans-total-RNA-Dauer-daf-2-91-hrs-post-L1-stage-25C-Rep1-4140-5.end1.100mers.fastq.bz2
