#sample_name strandededness input bam output_folder ############################################################################## #G88 ############################################################################## HJ-0001 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE101856/HJ-0001/fastq/tophat2/HJ-0001 _primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks HJ-0002 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE101856/HJ-0002/fastq/tophat2/HJ-0002_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks HJ-0003 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE101856/HJ-0003/fastq/tophat2/HJ-0003_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks HJ-0004 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE101856/HJ-0004/fastq/tophat2/HJ-0004_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks HJ-0005 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE101856/HJ-0005/fastq/tophat2/HJ-0005_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks HJ-0006 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE101856/HJ-0006/fastq/tophat2/HJ-0006_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks APAPL1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302/APAPL1/fastq/tophat2/APAPL1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks APAPL2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302/APAPL2/fastq/tophat2/APAPL2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks APAPL3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302/APAPL3/fastq/tophat2/APAPL3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks LRH-APAPL1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302/LRH-APAPL1/fastq/tophat2/LRH-APAPL1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks LRH-APAPL2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302/LRH-APAPL2/fastq/tophat2/LRH-APAPL2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks LRH-APAPL3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302/LRH-APAPL3/fastq/tophat2/LRH-APAPL3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks VL1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302/VL1/fastq/tophat2/VL1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks VL2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302/VL2/fastq/tophat2/VL2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks VL3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302/VL3/fastq/tophat2/VL3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1/fastq/tophat2/IC57-1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-2/fastq/tophat2/IC57-2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-3/fastq/tophat2/IC57-3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-4/fastq/tophat2/IC57-4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-6 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-6/fastq/tophat2/IC57-6_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-7 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-7/fastq/tophat2/IC57-7_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-8 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-8/fastq/tophat2/IC57-8_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-9 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-9/fastq/tophat2/IC57-9_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1149 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1149/fastq/tophat2/IC57-1149_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1150 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1150/fastq/tophat2/IC57-1150_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1151 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1151/fastq/tophat2/IC57-1151_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1152 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1152/fastq/tophat2/IC57-1152_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1159 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1159/fastq/tophat2/IC57-1159_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1160 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1160/fastq/tophat2/IC57-1160_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1161 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1161/fastq/tophat2/IC57-1161_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1162 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1162/fastq/tophat2/IC57-1162_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1164 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1164/fastq/tophat2/IC57-1164_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1165 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1165/fastq/tophat2/IC57-1165_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1166 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1166/fastq/tophat2/IC57-1166_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1167 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1167/fastq/tophat2/IC57-1167_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1169 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1169/fastq/tophat2/IC57-1169_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1170 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1170/fastq/tophat2/IC57-1170_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1171 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1171/fastq/tophat2/IC57-1171_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IC57-1172 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE111828/IC57-1172/fastq/tophat2/IC57-1172_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks I-R-1 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/I-R-1/fastq/tophat2/I-R-1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks I-R-2 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/I-R-2/fastq/tophat2/I-R-2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks I-R-3 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/I-R-3/fastq/tophat2/I-R-3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IPO-1 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/IPO-1/fastq/tophat2/IPO-1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IPO-2 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/IPO-2/fastq/tophat2/IPO-2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks IPO-3 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/IPO-3/fastq/tophat2/IPO-3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks N-1 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/N-1/fastq/tophat2/N-1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks N-2 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/N-2/fastq/tophat2/N-2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks N-3 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117066/N-3/fastq/tophat2/N-3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1h_MitoCDNB_1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/1h_MitoCDNB_1/fastq/tophat2/1h_MitoCDNB_1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1h_MitoCDNB_2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/1h_MitoCDNB_2/fastq/tophat2/1h_MitoCDNB_2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1h_MitoCDNB_3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/1h_MitoCDNB_3/fastq/tophat2/1h_MitoCDNB_3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1h_MitoCDNB_4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/1h_MitoCDNB_4/fastq/tophat2/1h_MitoCDNB_4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1h_MitoCDNB_5 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/1h_MitoCDNB_5/fastq/tophat2/1h_MitoCDNB_5_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1h_MitoCDNB_6 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/1h_MitoCDNB_6/fastq/tophat2/1h_MitoCDNB_6_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1h_Vehicle_1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/1h_Vehicle_1/fastq/tophat2/1h_Vehicle_1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1h_Vehicle_2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/1h_Vehicle_2/fastq/tophat2/1h_Vehicle_2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1h_Vehicle_3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/1h_Vehicle_3/fastq/tophat2/1h_Vehicle_3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1h_Vehicle_4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/1h_Vehicle_4/fastq/tophat2/1h_Vehicle_4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1h_Vehicle_5 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/1h_Vehicle_5/fastq/tophat2/1h_Vehicle_5_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1h_Vehicle_6 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/1h_Vehicle_6/fastq/tophat2/1h_Vehicle_6_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4h_MitoCDNB_1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/4h_MitoCDNB_1/fastq/tophat2/4h_MitoCDNB_1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4h_MitoCDNB_2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/4h_MitoCDNB_2/fastq/tophat2/4h_MitoCDNB_2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4h_MitoCDNB_3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/4h_MitoCDNB_3/fastq/tophat2/4h_MitoCDNB_3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4h_MitoCDNB_4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/4h_MitoCDNB_4/fastq/tophat2/4h_MitoCDNB_4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4h_MitoCDNB_5 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/4h_MitoCDNB_5/fastq/tophat2/4h_MitoCDNB_5_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4h_MitoCDNB_6 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/4h_MitoCDNB_6/fastq/tophat2/4h_MitoCDNB_6_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4h_Vehicle_1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/4h_Vehicle_1/fastq/tophat2/4h_Vehicle_1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4h_Vehicle_2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/4h_Vehicle_2/fastq/tophat2/4h_Vehicle_2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4h_Vehicle_3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/4h_Vehicle_3/fastq/tophat2/4h_Vehicle_3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4h_Vehicle_4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/4h_Vehicle_4/fastq/tophat2/4h_Vehicle_4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4h_Vehicle_5 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/4h_Vehicle_5/fastq/tophat2/4h_Vehicle_5_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4h_Vehicle_6 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117425/4h_Vehicle_6/fastq/tophat2/4h_Vehicle_6_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1_Liver_Basal_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/1_Liver_Basal_20/fastq/tophat2/1_Liver_Basal_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1_Liver_Low_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/1_Liver_Low_20/fastq/tophat2/1_Liver_Low_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1_Liver_High_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/1_Liver_High_20/fastq/tophat2/1_Liver_High_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1_Liver_Basal_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/1_Liver_Basal_3h/fastq/tophat2/1_Liver_Basal_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1_Liver_Low_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/1_Liver_Low_3h/fastq/tophat2/1_Liver_Low_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 1_Liver_High_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/1_Liver_High_3h/fastq/tophat2/1_Liver_High_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 2_Liver_Basal_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/2_Liver_Basal_20/fastq/tophat2/2_Liver_Basal_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 2_Liver_Low_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/2_Liver_Low_20/fastq/tophat2/2_Liver_Low_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 2_Liver_High_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/2_Liver_High_20/fastq/tophat2/2_Liver_High_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 2_Liver_Basal_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/2_Liver_Basal_3h/fastq/tophat2/2_Liver_Basal_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 2_Liver_Low_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/2_Liver_Low_3h/fastq/tophat2/2_Liver_Low_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 2_Liver_High_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/2_Liver_High_3h/fastq/tophat2/2_Liver_High_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 3_Liver_Basal_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/3_Liver_Basal_20/fastq/tophat2/3_Liver_Basal_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 3_Liver_Low_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/3_Liver_Low_20/fastq/tophat2/3_Liver_Low_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 3_Liver_High_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/3_Liver_High_20/fastq/tophat2/3_Liver_High_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 3_Liver_Basal_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/3_Liver_Basal_3h/fastq/tophat2/3_Liver_Basal_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 3_Liver_Low_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/3_Liver_Low_3h/fastq/tophat2/3_Liver_Low_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 3_Liver_High_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/3_Liver_High_3h/fastq/tophat2/3_Liver_High_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4_Liver_Basal_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/4_Liver_Basal_20/fastq/tophat2/4_Liver_Basal_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4_Liver_Low_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/4_Liver_Low_20/fastq/tophat2/4_Liver_Low_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4_Liver_High_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/4_Liver_High_20/fastq/tophat2/4_Liver_High_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4_Liver_Basal_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/4_Liver_Basal_3h/fastq/tophat2/4_Liver_Basal_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4_Liver_Low_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/4_Liver_Low_3h/fastq/tophat2/4_Liver_Low_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 4_Liver_High_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/4_Liver_High_3h/fastq/tophat2/4_Liver_High_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 5_Liver_Basal_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/5_Liver_Basal_20/fastq/tophat2/5_Liver_Basal_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 5_Liver_Low_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/5_Liver_Low_20/fastq/tophat2/5_Liver_Low_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 5_Liver_High_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/5_Liver_High_20/fastq/tophat2/5_Liver_High_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 5_Liver_Basal_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/5_Liver_Basal_3h/fastq/tophat2/5_Liver_Basal_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 6_Liver_Basal_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/6_Liver_Basal_20/fastq/tophat2/6_Liver_Basal_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 6_Liver_Low_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/6_Liver_Low_20/fastq/tophat2/6_Liver_Low_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 6_Liver_High_20 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/6_Liver_High_20/fastq/tophat2/6_Liver_High_20_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 6_Liver_Basal_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/6_Liver_Basal_3h/fastq/tophat2/6_Liver_Basal_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 6_Liver_Low_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/6_Liver_Low_3h/fastq/tophat2/6_Liver_Low_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks 6_Liver_High_3h fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE117741/6_Liver_High_3h/fastq/tophat2/6_Liver_High_3h_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Old-Cntrl-HTV1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Old-Cntrl-HTV1/fastq/tophat2/Old-Cntrl-HTV1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Old-Cntrl-HTV2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Old-Cntrl-HTV2/fastq/tophat2/Old-Cntrl-HTV2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Old-Cntrl-HTV3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Old-Cntrl-HTV3/fastq/tophat2/Old-Cntrl-HTV3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Old-Cntrl-HTV4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Old-Cntrl-HTV4/fastq/tophat2/Old-Cntrl-HTV4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Old-hMANF-HTV1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Old-hMANF-HTV1/fastq/tophat2/Old-hMANF-HTV1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Old-hMANF-HTV2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Old-hMANF-HTV2/fastq/tophat2/Old-hMANF-HTV2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Old-hMANF-HTV3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Old-hMANF-HTV3/fastq/tophat2/Old-hMANF-HTV3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Old-hMANF-HTV4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Old-hMANF-HTV4/fastq/tophat2/Old-hMANF-HTV4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg-Cntrl-HTV1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Yg-Cntrl-HTV1/fastq/tophat2/Yg-Cntrl-HTV1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg-Cntrl-HTV2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Yg-Cntrl-HTV2/fastq/tophat2/Yg-Cntrl-HTV2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg-Cntrl-HTV3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Yg-Cntrl-HTV3/fastq/tophat2/Yg-Cntrl-HTV3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg-Cntrl-HTV4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Yg-Cntrl-HTV4/fastq/tophat2/Yg-Cntrl-HTV4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg-hMANF-HTV1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Yg-hMANF-HTV1/fastq/tophat2/Yg-hMANF-HTV1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg-hMANF-HTV2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Yg-hMANF-HTV2/fastq/tophat2/Yg-hMANF-HTV2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg-hMANF-HTV3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Yg-hMANF-HTV3/fastq/tophat2/Yg-hMANF-HTV3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg-hMANF-HTV4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Yg-hMANF-HTV4/fastq/tophat2/Yg-hMANF-HTV4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O-O1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O-O1/fastq/tophat2/O-O1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O-O2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O-O2/fastq/tophat2/O-O2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O-O3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O-O3/fastq/tophat2/O-O3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O-O4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O-O4/fastq/tophat2/O-O4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O-O5 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O-O5/fastq/tophat2/O-O5_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O_YgHet_1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O_YgHet_1/fastq/tophat2/O_YgHet_1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O_YgHet_2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O_YgHet_2/fastq/tophat2/O_YgHet_2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O_YgHet_3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O_YgHet_3/fastq/tophat2/O_YgHet_3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O_YgHet_4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O_YgHet_4/fastq/tophat2/O_YgHet_4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O_YgHet_5 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O_YgHet_5/fastq/tophat2/O_YgHet_5_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O_YgWT_1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O_YgWT_1/fastq/tophat2/O_YgWT_1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O_YgWT_2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O_YgWT_2/fastq/tophat2/O_YgWT_2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O_YgWT_3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O_YgWT_3/fastq/tophat2/O_YgWT_3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O_YgWT_4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O_YgWT_4/fastq/tophat2/O_YgWT_4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks O_YgWT_5 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/O_YgWT_5/fastq/tophat2/O_YgWT_5_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg_Het1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Yg_Het1/fastq/tophat2/Yg_Het1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg_Het2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Yg_Het2/fastq/tophat2/Yg_Het2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg_Het3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Yg_Het3/fastq/tophat2/Yg_Het3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg_Het4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Yg_Het4/fastq/tophat2/Yg_Het4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg_Het5 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Yg_Het5/fastq/tophat2/Yg_Het5_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg_WT1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Yg_WT1/fastq/tophat2/Yg_WT1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg_WT2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Yg_WT2/fastq/tophat2/Yg_WT2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg_WT3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Yg_WT3/fastq/tophat2/Yg_WT3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg_WT4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Yg_WT4/fastq/tophat2/Yg_WT4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg_WT5 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123117/Yg_WT5/fastq/tophat2/Yg_WT5_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks GFP_1343 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/GFP_1343/fastq/tophat2/GFP_1343_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks GFP_1347 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/GFP_1347/fastq/tophat2/GFP_1347_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks GFP_1369 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/GFP_1369/fastq/tophat2/GFP_1369_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks GFP_1371 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/GFP_1371/fastq/tophat2/GFP_1371_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Nudt7_1357 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/Nudt7_1357/fastq/tophat2/Nudt7_1357_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Nudt7_1359 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/Nudt7_1359/fastq/tophat2/Nudt7_1359_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Nudt7_1365 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/Nudt7_1365/fastq/tophat2/Nudt7_1365_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Nudt7_2305 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/Nudt7_2305/fastq/tophat2/Nudt7_2305_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks CHOW1 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/CHOW1/fastq/tophat2/CHOW1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks CHOW2 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/CHOW2/fastq/tophat2/CHOW2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks CHOW3 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/CHOW3/fastq/tophat2/CHOW3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks NASH_OA-NO2_1 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/NASH_OA-NO2_1/fastq/tophat2/NASH_OA-NO2_1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks NASH_OA-NO2_2 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/NASH_OA-NO2_2/fastq/tophat2/NASH_OA-NO2_2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks NASH_OA-NO2_3 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/NASH_OA-NO2_3/fastq/tophat2/NASH_OA-NO2_3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks NASH_OA1 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/NASH_OA1/fastq/tophat2/NASH_OA1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks NASH_OA2 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/NASH_OA2/fastq/tophat2/NASH_OA2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks NASH_OA3 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/NASH_OA3/fastq/tophat2/NASH_OA3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks NASH_PEG1 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/NASH_PEG1/fastq/tophat2/NASH_PEG1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks NASH_PEG2 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/NASH_PEG2/fastq/tophat2/NASH_PEG2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks NASH_PEG3 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE126204/NASH_PEG3/fastq/tophat2/NASH_PEG3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks WT_1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/WT_1/fastq/tophat2/WT_1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks WT_2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/WT_2/fastq/tophat2/WT_2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks WT_3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/WT_3/fastq/tophat2/WT_3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks WT_4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/WT_4/fastq/tophat2/WT_4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks MANFHet_1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/MANFHet_1/fastq/tophat2/MANFHet_1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks MANFHet_2 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/MANFHet_2/fastq/tophat2/MANFHet_2_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks MANFHet_3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/MANFHet_3/fastq/tophat2/MANFHet_3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks MANFHet_4 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123116/MANFHet_4/fastq/tophat2/MANFHet_4_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks LRH-APAPL3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE104302/LRH-APAPL3/fastq/tophat2/LRH-APAPL3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg-Cntrl-HTV1 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Yg-Cntrl-HTV1/fastq/tophat2/Yg-Cntrl-HTV1_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks Yg-Cntrl-HTV3 fr-firststrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE123115/Yg-Cntrl-HTV3/fastq/tophat2/Yg-Cntrl-HTV3_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks GFP_1343 fr-secondstrand /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/GSE125237/GFP_1343/fastq/tophat2/GFP_1343_primary_unique.bam /restricted/projectnb/waxmanlab/varsha/cufflinks