/share/pkg.7/cufflinks/2.2.1/install/bin/cuffmerge -o /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/results_tisha -g /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/genes.gtf -s /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/genomeWithRandom.fa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/assemblies.txt