cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_1 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031887/accepted_hits.bam,tophat_out/SRR031928/accepted_hits.bam,tophat_out/SRR031966/accepted_hits.bam,tophat_out/SRR031890/accepted_hits.bam,tophat_out/SRR031827/accepted_hits.bam tophat_out/SRR031923/accepted_hits.bam,tophat_out/SRR031910/accepted_hits.bam,tophat_out/SRR031935/accepted_hits.bam,tophat_out/SRR031970/accepted_hits.bam,tophat_out/SRR031826/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_2 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031890/accepted_hits.bam,tophat_out/SRR031911/accepted_hits.bam,tophat_out/SRR031891/accepted_hits.bam,tophat_out/SRR031921/accepted_hits.bam,tophat_out/SRR031887/accepted_hits.bam tophat_out/SRR031830/accepted_hits.bam,tophat_out/SRR031969/accepted_hits.bam,tophat_out/SRR031924/accepted_hits.bam,tophat_out/SRR031905/accepted_hits.bam,tophat_out/SRR031922/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_3 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031969/accepted_hits.bam,tophat_out/SRR031929/accepted_hits.bam,tophat_out/SRR031830/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam,tophat_out/SRR031827/accepted_hits.bam tophat_out/SRR031905/accepted_hits.bam,tophat_out/SRR031892/accepted_hits.bam,tophat_out/SRR031970/accepted_hits.bam,tophat_out/SRR031965/accepted_hits.bam,tophat_out/SRR031924/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_4 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031911/accepted_hits.bam,tophat_out/SRR031826/accepted_hits.bam,tophat_out/SRR031890/accepted_hits.bam,tophat_out/SRR031825/accepted_hits.bam,tophat_out/SRR031966/accepted_hits.bam tophat_out/SRR031905/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam,tophat_out/SRR031910/accepted_hits.bam,tophat_out/SRR031969/accepted_hits.bam,tophat_out/SRR031928/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_5 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031965/accepted_hits.bam,tophat_out/SRR031887/accepted_hits.bam,tophat_out/SRR031935/accepted_hits.bam,tophat_out/SRR031911/accepted_hits.bam,tophat_out/SRR031969/accepted_hits.bam tophat_out/SRR031910/accepted_hits.bam,tophat_out/SRR031923/accepted_hits.bam,tophat_out/SRR031826/accepted_hits.bam,tophat_out/SRR031922/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_6 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031905/accepted_hits.bam,tophat_out/SRR031922/accepted_hits.bam,tophat_out/SRR031966/accepted_hits.bam,tophat_out/SRR031969/accepted_hits.bam,tophat_out/SRR031935/accepted_hits.bam tophat_out/SRR031891/accepted_hits.bam,tophat_out/SRR031830/accepted_hits.bam,tophat_out/SRR031930/accepted_hits.bam,tophat_out/SRR031829/accepted_hits.bam,tophat_out/SRR031827/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_7 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031924/accepted_hits.bam,tophat_out/SRR031830/accepted_hits.bam,tophat_out/SRR031935/accepted_hits.bam,tophat_out/SRR031966/accepted_hits.bam,tophat_out/SRR031965/accepted_hits.bam tophat_out/SRR031929/accepted_hits.bam,tophat_out/SRR031928/accepted_hits.bam,tophat_out/SRR031827/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam,tophat_out/SRR031922/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_8 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031965/accepted_hits.bam,tophat_out/SRR031929/accepted_hits.bam,tophat_out/SRR031829/accepted_hits.bam,tophat_out/SRR031930/accepted_hits.bam,tophat_out/SRR031825/accepted_hits.bam tophat_out/SRR031966/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam,tophat_out/SRR031921/accepted_hits.bam,tophat_out/SRR031891/accepted_hits.bam,tophat_out/SRR031887/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_9 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031970/accepted_hits.bam,tophat_out/SRR031935/accepted_hits.bam,tophat_out/SRR031830/accepted_hits.bam,tophat_out/SRR031827/accepted_hits.bam,tophat_out/SRR031905/accepted_hits.bam tophat_out/SRR031826/accepted_hits.bam,tophat_out/SRR031930/accepted_hits.bam,tophat_out/SRR031923/accepted_hits.bam,tophat_out/SRR031887/accepted_hits.bam,tophat_out/SRR031965/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_10 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031929/accepted_hits.bam,tophat_out/SRR031892/accepted_hits.bam,tophat_out/SRR031830/accepted_hits.bam,tophat_out/SRR031970/accepted_hits.bam,tophat_out/SRR031890/accepted_hits.bam tophat_out/SRR031928/accepted_hits.bam,tophat_out/SRR031969/accepted_hits.bam,tophat_out/SRR031911/accepted_hits.bam,tophat_out/SRR031966/accepted_hits.bam,tophat_out/SRR031891/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_11 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031970/accepted_hits.bam,tophat_out/SRR031929/accepted_hits.bam,tophat_out/SRR031922/accepted_hits.bam,tophat_out/SRR031965/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam tophat_out/SRR031891/accepted_hits.bam,tophat_out/SRR031887/accepted_hits.bam,tophat_out/SRR031905/accepted_hits.bam,tophat_out/SRR031935/accepted_hits.bam,tophat_out/SRR031930/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_12 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031830/accepted_hits.bam,tophat_out/SRR031921/accepted_hits.bam,tophat_out/SRR031929/accepted_hits.bam,tophat_out/SRR031890/accepted_hits.bam,tophat_out/SRR031905/accepted_hits.bam tophat_out/SRR031891/accepted_hits.bam,tophat_out/SRR031965/accepted_hits.bam,tophat_out/SRR031826/accepted_hits.bam,tophat_out/SRR031910/accepted_hits.bam,tophat_out/SRR031827/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_13 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031829/accepted_hits.bam,tophat_out/SRR031970/accepted_hits.bam,tophat_out/SRR031930/accepted_hits.bam,tophat_out/SRR031935/accepted_hits.bam,tophat_out/SRR031887/accepted_hits.bam tophat_out/SRR031825/accepted_hits.bam,tophat_out/SRR031922/accepted_hits.bam,tophat_out/SRR031969/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam,tophat_out/SRR031965/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_14 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031905/accepted_hits.bam,tophat_out/SRR031830/accepted_hits.bam,tophat_out/SRR031825/accepted_hits.bam,tophat_out/SRR031930/accepted_hits.bam,tophat_out/SRR031892/accepted_hits.bam tophat_out/SRR031969/accepted_hits.bam,tophat_out/SRR031826/accepted_hits.bam,tophat_out/SRR031891/accepted_hits.bam,tophat_out/SRR031890/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_15 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031910/accepted_hits.bam,tophat_out/SRR031887/accepted_hits.bam,tophat_out/SRR031905/accepted_hits.bam,tophat_out/SRR031935/accepted_hits.bam,tophat_out/SRR031922/accepted_hits.bam tophat_out/SRR031923/accepted_hits.bam,tophat_out/SRR031969/accepted_hits.bam,tophat_out/SRR031911/accepted_hits.bam,tophat_out/SRR031929/accepted_hits.bam,tophat_out/SRR031928/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_16 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031910/accepted_hits.bam,tophat_out/SRR031923/accepted_hits.bam,tophat_out/SRR031935/accepted_hits.bam,tophat_out/SRR031826/accepted_hits.bam,tophat_out/SRR031911/accepted_hits.bam tophat_out/SRR031922/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam,tophat_out/SRR031887/accepted_hits.bam,tophat_out/SRR031830/accepted_hits.bam,tophat_out/SRR031969/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_17 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031929/accepted_hits.bam,tophat_out/SRR031892/accepted_hits.bam,tophat_out/SRR031825/accepted_hits.bam,tophat_out/SRR031935/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam tophat_out/SRR031921/accepted_hits.bam,tophat_out/SRR031905/accepted_hits.bam,tophat_out/SRR031829/accepted_hits.bam,tophat_out/SRR031966/accepted_hits.bam,tophat_out/SRR031924/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_18 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031887/accepted_hits.bam,tophat_out/SRR031969/accepted_hits.bam,tophat_out/SRR031970/accepted_hits.bam,tophat_out/SRR031825/accepted_hits.bam,tophat_out/SRR031890/accepted_hits.bam tophat_out/SRR031929/accepted_hits.bam,tophat_out/SRR031892/accepted_hits.bam,tophat_out/SRR031935/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam,tophat_out/SRR031826/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_19 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031965/accepted_hits.bam,tophat_out/SRR031929/accepted_hits.bam,tophat_out/SRR031829/accepted_hits.bam,tophat_out/SRR031910/accepted_hits.bam,tophat_out/SRR031923/accepted_hits.bam tophat_out/SRR031826/accepted_hits.bam,tophat_out/SRR031924/accepted_hits.bam,tophat_out/SRR031830/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam,tophat_out/SRR031827/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_20 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031928/accepted_hits.bam,tophat_out/SRR031930/accepted_hits.bam,tophat_out/SRR031892/accepted_hits.bam,tophat_out/SRR031965/accepted_hits.bam,tophat_out/SRR031890/accepted_hits.bam tophat_out/SRR031966/accepted_hits.bam,tophat_out/SRR031969/accepted_hits.bam,tophat_out/SRR031911/accepted_hits.bam,tophat_out/SRR031970/accepted_hits.bam,tophat_out/SRR031910/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_21 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031825/accepted_hits.bam,tophat_out/SRR031829/accepted_hits.bam,tophat_out/SRR031965/accepted_hits.bam,tophat_out/SRR031924/accepted_hits.bam,tophat_out/SRR031966/accepted_hits.bam tophat_out/SRR031910/accepted_hits.bam,tophat_out/SRR031911/accepted_hits.bam,tophat_out/SRR031970/accepted_hits.bam,tophat_out/SRR031892/accepted_hits.bam,tophat_out/SRR031830/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_22 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031965/accepted_hits.bam,tophat_out/SRR031930/accepted_hits.bam,tophat_out/SRR031905/accepted_hits.bam,tophat_out/SRR031910/accepted_hits.bam,tophat_out/SRR031825/accepted_hits.bam tophat_out/SRR031890/accepted_hits.bam,tophat_out/SRR031830/accepted_hits.bam,tophat_out/SRR031826/accepted_hits.bam,tophat_out/SRR031924/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_23 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031830/accepted_hits.bam,tophat_out/SRR031910/accepted_hits.bam,tophat_out/SRR031966/accepted_hits.bam,tophat_out/SRR031887/accepted_hits.bam,tophat_out/SRR031965/accepted_hits.bam tophat_out/SRR031924/accepted_hits.bam,tophat_out/SRR031970/accepted_hits.bam,tophat_out/SRR031923/accepted_hits.bam,tophat_out/SRR031826/accepted_hits.bam,tophat_out/SRR031827/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_24 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031935/accepted_hits.bam,tophat_out/SRR031827/accepted_hits.bam,tophat_out/SRR031826/accepted_hits.bam,tophat_out/SRR031965/accepted_hits.bam,tophat_out/SRR031923/accepted_hits.bam tophat_out/SRR031829/accepted_hits.bam,tophat_out/SRR031905/accepted_hits.bam,tophat_out/SRR031825/accepted_hits.bam,tophat_out/SRR031891/accepted_hits.bam,tophat_out/SRR031922/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_25 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031966/accepted_hits.bam,tophat_out/SRR031830/accepted_hits.bam,tophat_out/SRR031930/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam,tophat_out/SRR031826/accepted_hits.bam tophat_out/SRR031910/accepted_hits.bam,tophat_out/SRR031825/accepted_hits.bam,tophat_out/SRR031827/accepted_hits.bam,tophat_out/SRR031923/accepted_hits.bam,tophat_out/SRR031970/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_26 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031924/accepted_hits.bam,tophat_out/SRR031827/accepted_hits.bam,tophat_out/SRR031891/accepted_hits.bam,tophat_out/SRR031829/accepted_hits.bam,tophat_out/SRR031930/accepted_hits.bam tophat_out/SRR031826/accepted_hits.bam,tophat_out/SRR031935/accepted_hits.bam,tophat_out/SRR031929/accepted_hits.bam,tophat_out/SRR031965/accepted_hits.bam,tophat_out/SRR031910/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_27 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031969/accepted_hits.bam,tophat_out/SRR031910/accepted_hits.bam,tophat_out/SRR031825/accepted_hits.bam,tophat_out/SRR031887/accepted_hits.bam,tophat_out/SRR031827/accepted_hits.bam tophat_out/SRR031965/accepted_hits.bam,tophat_out/SRR031892/accepted_hits.bam,tophat_out/SRR031966/accepted_hits.bam,tophat_out/SRR031922/accepted_hits.bam,tophat_out/SRR031905/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_28 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031928/accepted_hits.bam,tophat_out/SRR031892/accepted_hits.bam,tophat_out/SRR031923/accepted_hits.bam,tophat_out/SRR031830/accepted_hits.bam,tophat_out/SRR031827/accepted_hits.bam tophat_out/SRR031965/accepted_hits.bam,tophat_out/SRR031969/accepted_hits.bam,tophat_out/SRR031891/accepted_hits.bam,tophat_out/SRR031910/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_29 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031887/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam,tophat_out/SRR031911/accepted_hits.bam,tophat_out/SRR031890/accepted_hits.bam,tophat_out/SRR031965/accepted_hits.bam tophat_out/SRR031829/accepted_hits.bam,tophat_out/SRR031924/accepted_hits.bam,tophat_out/SRR031923/accepted_hits.bam,tophat_out/SRR031966/accepted_hits.bam,tophat_out/SRR031929/accepted_hits.bam
cuffdiff -q -p 8 --no-js-test -o cuffdiff_results/cuffdiff_random_30 /tophatindices/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf tophat_out/SRR031892/accepted_hits.bam,tophat_out/SRR031928/accepted_hits.bam,tophat_out/SRR031921/accepted_hits.bam,tophat_out/SRR031923/accepted_hits.bam,tophat_out/SRR031971/accepted_hits.bam tophat_out/SRR031905/accepted_hits.bam,tophat_out/SRR031826/accepted_hits.bam,tophat_out/SRR031825/accepted_hits.bam,tophat_out/SRR031887/accepted_hits.bam,tophat_out/SRR031966/accepted_hits.bam