/share/pkg.7/cufflinks/2.2.1/install/bin/cuffmerge -o /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test -g /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/genes.gtf -s /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/genomeWithRandom.fa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/assemblies.txt
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/HJ-0002_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileQNxFrr
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/HJ-0003_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileacla31
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/HJ-0004_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileFSbz1S
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/HJ-0005_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileNUcOjZ
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/HJ-0006_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filepqdwDl
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/APAPL1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevJrtEZ
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/APAPL2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileFhkoaT
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/APAPL3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filedkEhJ1
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/LRH-APAPL1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file9AonPp
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/LRH-APAPL2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileK6Op33
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/LRH-APAPL3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filebK9AYX
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/VL1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileTdNVD7
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/VL2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filelo6w8w
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/VL3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileJLE15b
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileILzqG6
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filexRpeYe
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileRLmHMA
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileYvlyta
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-6_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileOWILcX
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-7_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileZjh33W
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-8_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file6krJda
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-9_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileCXhDTA
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1149_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file6rTGKe
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1150_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filetCMMV5
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1151_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileShz609
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1152_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevqoppr
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1159_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevNZnnW
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1160_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filenh5XDF
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1161_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileMTaTzC
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1162_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filep52E7M
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1164_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileNF6wAa
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1165_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filetUKmlL
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1166_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file8xSTMz
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1167_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileaRp3AB
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1169_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filenKdzSQ
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1170_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filePWjdxj
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1171_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filegSJLWZ
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IC57-1172_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileUVj8IT
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/I-R-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file6o8Dg0
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/I-R-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filedMzSBj
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/I-R-3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileiY0KXP
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IPO-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filePRCoqz
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IPO-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file4uwtRv
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/IPO-3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filesGRI0E
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/N-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileGb5wM0
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/N-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevf9pdz
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/N-3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileN3YG3k
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1h_MitoCDNB_1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileTCiock
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1h_MitoCDNB_2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filecBSQey
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1h_MitoCDNB_3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filer6wLK0
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1h_MitoCDNB_4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filepJXaRH
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1h_MitoCDNB_5_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file64ACMD
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1h_MitoCDNB_6_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileUnVrBO
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1h_Vehicle_1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileZpeUce
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1h_Vehicle_2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileiZ9cES
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1h_Vehicle_3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file4cutsL
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1h_Vehicle_4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filezykyOS
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1h_Vehicle_5_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileUb40Ee
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1h_Vehicle_6_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileImRbeP
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4h_MitoCDNB_1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXv8DyE
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4h_MitoCDNB_2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filef6SZyI
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4h_MitoCDNB_3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileqvwfx1
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4h_MitoCDNB_4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filePvtnbz
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4h_MitoCDNB_5_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file6FJOMl
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4h_MitoCDNB_6_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filedeR1on
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4h_Vehicle_1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file73PS0D
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4h_Vehicle_2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXKoRn9
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4h_Vehicle_3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filesPCGoT
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4h_Vehicle_4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXRLwnS
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4h_Vehicle_5_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileW4eyn6
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4h_Vehicle_6_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileMBPFmz
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1_Liver_Basal_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filenoACih
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1_Liver_Low_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file6Rhdsc
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1_Liver_High_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileFGhMPl
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1_Liver_Basal_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevjoTtJ
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1_Liver_Low_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileNYX4Rk
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/1_Liver_High_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileWidW6a
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/2_Liver_Basal_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXWL0Ef
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/2_Liver_Low_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filew0E7Zx
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/2_Liver_High_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filem6y503
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/2_Liver_Basal_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file9BN6fN
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/2_Liver_Low_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file9j0lvJ
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/2_Liver_High_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileNywjAT
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/3_Liver_Basal_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileKS9jAg
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/3_Liver_Low_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileC9QRvR
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/3_Liver_High_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileY6tBlF
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/3_Liver_Basal_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileN6me2G
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/3_Liver_Low_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileuj8zJV
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/3_Liver_High_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filehJ09Jo
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4_Liver_Basal_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXxyNq5
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4_Liver_Low_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filel8v9XY
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4_Liver_High_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filezz7XA5
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4_Liver_Basal_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileNlstLq
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4_Liver_Low_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileD9UKxZ
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/4_Liver_High_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevdMctL
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/5_Liver_Basal_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filepxxTJL
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/5_Liver_Low_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filel8kKGZ
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/5_Liver_High_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileMPqqNq
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/5_Liver_Basal_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevGfGp6
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/6_Liver_Basal_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileLfjPTZ
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/6_Liver_Low_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filehDE2n7
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/6_Liver_High_20_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file65LLNr
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/6_Liver_Basal_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filekOB59Z
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/6_Liver_Low_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filegbjwuL
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/6_Liver_High_3h_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filetEpVfK
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Old-Cntrl-HTV1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filev6U5LV
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Old-Cntrl-HTV2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileMUutMm
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Old-Cntrl-HTV3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filewHbFz3
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Old-Cntrl-HTV4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileX1bMh0
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Old-hMANF-HTV1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileV9pOLc
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Old-hMANF-HTV2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileW9SiVE
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Old-hMANF-HTV3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file4t9LPm
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Old-hMANF-HTV4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileNiUF1m
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg-Cntrl-HTV1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileafq7PC
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg-Cntrl-HTV2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileCWDmk8
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg-Cntrl-HTV3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXzBvxT
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg-Cntrl-HTV4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileuoCnhU
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg-hMANF-HTV1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileDQXrUa
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg-hMANF-HTV2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileSXkMxH
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg-hMANF-HTV3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevZfjct
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg-hMANF-HTV4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileFqKdXt
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O-O1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXulhbL
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O-O2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileghY15h
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O-O3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileeH4qh5
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O-O4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileVDodB8
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O-O5_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevzYEMs
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O_YgHet_1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileqkPCt2
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O_YgHet_2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileZlw4IR
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O_YgHet_3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileCaOvyW
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O_YgHet_4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileVFn7Wg
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O_YgHet_5_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileCWaKQQ
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O_YgWT_1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileMh1NfG
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O_YgWT_2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filezDw1JL
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O_YgWT_3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filezei946
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O_YgWT_4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file1dhW9H
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/O_YgWT_5_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileEfWOfz
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg_Het1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filezkuL3F
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg_Het2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileTlWQs2
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg_Het3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileM3cWcE
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg_Het4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileifPjGv
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg_Het5_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileK5gHfC
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg_WT1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filek7zEgY
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg_WT2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file4t6QgA
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg_WT3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileVhjxYs
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg_WT4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filettdduB
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Yg_WT5_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileyHGANZ
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/GFP_1343_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filesypqSD
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/GFP_1347_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXv8Tfw
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/GFP_1369_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileVp8e1C
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/GFP_1371_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileiLGFlY
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Nudt7_1357_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevgZ6fy
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Nudt7_1359_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileYH1jsm
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Nudt7_1365_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileIM0yoo
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/Nudt7_2305_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filenMzfmE
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CHOW1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileqd10S8
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CHOW2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file2Bbg1Q
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CHOW3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filezrPXaM
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/NASH_OA-NO2_1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filepR5I2U
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/NASH_OA-NO2_2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileUKvweh
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/NASH_OA-NO2_3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filesN0WYQ
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/NASH_OA1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileR9UvQD
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/NASH_OA2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileFnf1AD
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/NASH_OA3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filejw4QdQ
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/NASH_PEG1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileO97y7f
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/NASH_PEG2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileTu7Z4S
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/NASH_PEG3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file3Je3DJ
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/WT_1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileghsmqN
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/WT_2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filek2yZx7
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/WT_3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_files3idCH
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/WT_4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileBbVSVx
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/MANFHet_1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileUI7jbE
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/MANFHet_2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileHEvDv0
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/MANFHet_3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filemDlQvC
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/MANFHet_4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileQ2JmVt
sort -k 3,3 -k 4,4n --temporary-directory=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileQNxFrr /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileacla31 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileFSbz1S /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileNUcOjZ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filepqdwDl /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevJrtEZ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileFhkoaT /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filedkEhJ1 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file9AonPp /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileK6Op33 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filebK9AYX /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileTdNVD7 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filelo6w8w /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileJLE15b /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileILzqG6 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filexRpeYe /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileRLmHMA /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileYvlyta /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileOWILcX /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileZjh33W /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file6krJda /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileCXhDTA /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file6rTGKe /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filetCMMV5 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileShz609 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevqoppr /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevNZnnW /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filenh5XDF /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileMTaTzC /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filep52E7M /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileNF6wAa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filetUKmlL /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file8xSTMz /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileaRp3AB /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filenKdzSQ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filePWjdxj /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filegSJLWZ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileUVj8IT /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file6o8Dg0 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filedMzSBj /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileiY0KXP /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filePRCoqz /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file4uwtRv /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filesGRI0E /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileGb5wM0 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevf9pdz /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileN3YG3k /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileTCiock /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filecBSQey /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filer6wLK0 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filepJXaRH /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file64ACMD /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileUnVrBO /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileZpeUce /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileiZ9cES /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file4cutsL /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filezykyOS /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileUb40Ee /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileImRbeP /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXv8DyE /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filef6SZyI /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileqvwfx1 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filePvtnbz /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file6FJOMl /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filedeR1on /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file73PS0D /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXKoRn9 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filesPCGoT /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXRLwnS /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileW4eyn6 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileMBPFmz /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filenoACih /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file6Rhdsc /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileFGhMPl /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevjoTtJ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileNYX4Rk /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileWidW6a /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXWL0Ef /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filew0E7Zx /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filem6y503 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file9BN6fN /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file9j0lvJ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileNywjAT /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileKS9jAg /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileC9QRvR /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileY6tBlF /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileN6me2G /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileuj8zJV /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filehJ09Jo /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXxyNq5 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filel8v9XY /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filezz7XA5 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileNlstLq /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileD9UKxZ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevdMctL /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filepxxTJL /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filel8kKGZ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileMPqqNq /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevGfGp6 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileLfjPTZ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filehDE2n7 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file65LLNr /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filekOB59Z /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filegbjwuL /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filetEpVfK /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filev6U5LV /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileMUutMm /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filewHbFz3 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileX1bMh0 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileV9pOLc /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileW9SiVE /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file4t9LPm /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileNiUF1m /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileafq7PC /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileCWDmk8 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXzBvxT /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileuoCnhU /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileDQXrUa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileSXkMxH /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevZfjct /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileFqKdXt /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXulhbL /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileghY15h /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileeH4qh5 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileVDodB8 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevzYEMs /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileqkPCt2 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileZlw4IR /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileCaOvyW /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileVFn7Wg /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileCWaKQQ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileMh1NfG /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filezDw1JL /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filezei946 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file1dhW9H /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileEfWOfz /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filezkuL3F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileTlWQs2 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileM3cWcE /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileifPjGv /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileK5gHfC /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filek7zEgY /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file4t6QgA /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileVhjxYs /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filettdduB /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileyHGANZ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filesypqSD /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileXv8Tfw /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileVp8e1C /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileiLGFlY /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filevgZ6fy /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileYH1jsm /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileIM0yoo /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filenMzfmE /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileqd10S8 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file2Bbg1Q /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filezrPXaM /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filepR5I2U /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileUKvweh /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filesN0WYQ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileR9UvQD /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileFnf1AD /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filejw4QdQ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileO97y7f /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileTu7Z4S /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_file3Je3DJ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileghsmqN /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filek2yZx7 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_files3idCH /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileBbVSVx /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileUI7jbE /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileHEvDv0 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_filemDlQvC /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/gtf2sam_fileQ2JmVt > /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/mergeSam_fileqx1T4B
cufflinks -o /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/ -F 0.05 -g /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/genes.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 1 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test/tmp/mergeSam_fileqx1T4B
cuffcompare -o tmp_meta_asm -C -G  -r /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/genes.gtf  -s /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/genomeWithRandom.fa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test//transcripts.gtf
cuffcompare -o tmp_meta_asm -C -G  -r /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/genes.gtf  -s /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/genomeWithRandom.fa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmer_test//merged.gtf