cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_1 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_1 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_2 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_2 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_3 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_3 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_4 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_4 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_5 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_5 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_6 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_6 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_7 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_7 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_8 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_8 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_9 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_9 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_10 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_10 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_11 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_11 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_12 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_12 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_13 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_13 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_14 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_14 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_15 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_15 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_16 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_16 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_17 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_17 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_18 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_18 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_19 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_19 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_20 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_20 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_21 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_21 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_22 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_22 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_23 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_23 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_24 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_24 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_25 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_25 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_26 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_26 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_27 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_27 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_28 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_28 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_29 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_29 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_testset_30 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099227/accepted_hits.bam,tophat_out/SRR099233/accepted_hits.bam,tophat_out/SRR099238/accepted_hits.bam tophat_out/SRR099224/accepted_hits.bam,tophat_out/SRR099236/accepted_hits.bam,tophat_out/SRR099240/accepted_hits.bam 
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_heldoutset_30 /tophatindices/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes.gtf tophat_out/SRR099228/accepted_hits.bam,tophat_out/SRR099229/accepted_hits.bam,tophat_out/SRR099230/accepted_hits.bam,tophat_out/SRR099231/accepted_hits.bam,tophat_out/SRR099232/accepted_hits.bam,tophat_out/SRR099237/accepted_hits.bam,tophat_out/SRR099239/accepted_hits.bam tophat_out/SRR099223/accepted_hits.bam,tophat_out/SRR099225/accepted_hits.bam,tophat_out/SRR099226/accepted_hits.bam,tophat_out/SRR099234/accepted_hits.bam,tophat_out/SRR099235/accepted_hits.bam,tophat_out/SRR099241/accepted_hits.bam,tophat_out/SRR099242/accepted_hits.bam,tophat_out/SRR099243/accepted_hits.bam