/share/pkg.7/cufflinks/2.2.1/install/bin/cuffmerge -o /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new -g /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/genes.gtf -s /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/genomeWithRandom.fa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/assemblies.txt
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/ncRNA_exon_for_counting.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filexa3lOU
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/HJ-0001_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileWitpKT
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/cuffmerge_withkk/new/tmp/gtf2sam_fileHZ5Fe8
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/cuffmerge_withkk/new/tmp/gtf2sam_fileMSIOFF
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/cuffmerge_withkk/new/tmp/gtf2sam_fileBNS8lu
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/cuffmerge_withkk/new/tmp/gtf2sam_filePZ4YMy
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/cuffmerge_withkk/new/tmp/gtf2sam_file6GF48T
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/cuffmerge_withkk/new/tmp/gtf2sam_fileEvw8ox
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/cuffmerge_withkk/new/tmp/gtf2sam_fileMiodRq
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/cuffmerge_withkk/new/tmp/gtf2sam_filegLtnXz
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/cuffmerge_withkk/new/tmp/gtf2sam_file8wXVVY
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/cuffmerge_withkk/new/tmp/gtf2sam_fileyYrlTD
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/cuffmerge_withkk/new/tmp/gtf2sam_fileuxEB9z
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/cuffmerge_withkk/new/tmp/gtf2sam_file6hm63L
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/cuffmerge_withkk/new/tmp/gtf2sam_file9cSQEd
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/cuffmerge_withkk/new/tmp/gtf2sam_fileJICyOU
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/cuffmerge_withkk/new/tmp/gtf2sam_fileZsiNzR
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/cuffmerge_withkk/new/tmp/gtf2sam_file0iA3I2
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/cuffmerge_withkk/new/tmp/gtf2sam_file2N18vr
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/cuffmerge_withkk/new/tmp/gtf2sam_fileNCIbk4
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/cuffmerge_withkk/new/tmp/gtf2sam_filekhrD7T
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/cuffmerge_withkk/new/tmp/gtf2sam_filexRXstX
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/cuffmerge_withkk/new/tmp/gtf2sam_fileLHbPJe
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/cuffmerge_withkk/new/tmp/gtf2sam_filekp61EJ
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/cuffmerge_withkk/new/tmp/gtf2sam_fileTIoLYr
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/cuffmerge_withkk/new/tmp/gtf2sam_fileMLhXmo
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/cuffmerge_withkk/new/tmp/gtf2sam_fileWIVFfy
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/cuffmerge_withkk/new/tmp/gtf2sam_fileeQaDaW
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/cuffmerge_withkk/new/tmp/gtf2sam_fileJ2yiSx
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/cuffmerge_withkk/new/tmp/gtf2sam_fileQm1Y4o
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/cuffmerge_withkk/new/tmp/gtf2sam_fileFfhWEv
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/cuffmerge_withkk/new/tmp/gtf2sam_filehyzQ2P
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/cuffmerge_withkk/new/tmp/gtf2sam_filegtQvRp
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/cuffmerge_withkk/new/tmp/gtf2sam_fileZnVwid
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/cuffmerge_withkk/new/tmp/gtf2sam_filedBpUue
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/cuffmerge_withkk/new/tmp/gtf2sam_file8zjBmt
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/cuffmerge_withkk/new/tmp/gtf2sam_fileZqV4TV
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/cuffmerge_withkk/new/tmp/gtf2sam_filez5RiOB
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/cuffmerge_withkk/new/tmp/gtf2sam_file0tIZ8u
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/cuffmerge_withkk/new/tmp/gtf2sam_fileZcFw8B
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/cuffmerge_withkk/new/tmp/gtf2sam_filePvxCKW
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/cuffmerge_withkk/new/tmp/gtf2sam_fileJWdGBu
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/cuffmerge_withkk/new/tmp/gtf2sam_fileQGmf2f
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/cuffmerge_withkk/new/tmp/gtf2sam_fileKjVaFe
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/cuffmerge_withkk/new/tmp/gtf2sam_fileHS6Srq
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/cuffmerge_withkk/new/tmp/gtf2sam_filerqklwP
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/cuffmerge_withkk/new/tmp/gtf2sam_filea2TVyr
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/cuffmerge_withkk/new/tmp/gtf2sam_filexDJzPg
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/cuffmerge_withkk/new/tmp/gtf2sam_filewulKCj
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/cuffmerge_withkk/new/tmp/gtf2sam_fileWGQdaA
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/cuffmerge_withkk/new/tmp/gtf2sam_filendGE35
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/cuffmerge_withkk/new/tmp/gtf2sam_fileM2G3XQ
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/cuffmerge_withkk/new/tmp/gtf2sam_fileFj0DFQ
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/cuffmerge_withkk/new/tmp/gtf2sam_filehegHr5
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/cuffmerge_withkk/new/tmp/gtf2sam_fileZxu5fz
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/cuffmerge_withkk/new/tmp/gtf2sam_fileOaRYIj
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/cuffmerge_withkk/new/tmp/gtf2sam_file3O6Mbj
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/cuffmerge_withkk/new/tmp/gtf2sam_file9Tk1xx
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/cuffmerge_withkk/new/tmp/gtf2sam_file0m5yH0
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/cuffmerge_withkk/new/tmp/gtf2sam_fileXVMgAK
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/cuffmerge_withkk/new/tmp/gtf2sam_file0QYlzJ
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/cuffmerge_withkk/new/tmp/gtf2sam_filetsN8GX
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/cuffmerge_withkk/new/tmp/gtf2sam_fileJoCwUq
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/cuffmerge_withkk/new/tmp/gtf2sam_fileMqCFJa
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/cuffmerge_withkk/new/tmp/gtf2sam_fileIhpjt9
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/cuffmerge_withkk/new/tmp/gtf2sam_file32s9ln
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/cuffmerge_withkk/new/tmp/gtf2sam_fileAqRlqQ
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/cuffmerge_withkk/new/tmp/gtf2sam_fileY0Nupy
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/cuffmerge_withkk/new/tmp/gtf2sam_filefvy7Gv
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/cuffmerge_withkk/new/tmp/gtf2sam_filef0rdQH
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/cuffmerge_withkk/new/tmp/gtf2sam_file1mOJR8
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/cuffmerge_withkk/new/tmp/gtf2sam_fileeh4PwP
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/cuffmerge_withkk/new/tmp/gtf2sam_filehFibGL
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/cuffmerge_withkk/new/tmp/gtf2sam_filefsPXhX
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/cuffmerge_withkk/new/tmp/gtf2sam_fileykU8Sl
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/cuffmerge_withkk/new/tmp/gtf2sam_file1UQgvY
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/cuffmerge_withkk/new/tmp/gtf2sam_fileUwsnHP
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/cuffmerge_withkk/new/tmp/gtf2sam_files1SiDT
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/cuffmerge_withkk/new/tmp/gtf2sam_filexdtogb
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/cuffmerge_withkk/new/tmp/gtf2sam_fileThIrUG
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/cuffmerge_withkk/new/tmp/gtf2sam_fileiMuyFq
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/cuffmerge_withkk/new/tmp/gtf2sam_fileKTL1bo
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/cuffmerge_withkk/new/tmp/gtf2sam_filev7ZuOy
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/cuffmerge_withkk/new/tmp/gtf2sam_filepIR9tW
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/cuffmerge_withkk/new/tmp/gtf2sam_file7et02x
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/cuffmerge_withkk/new/tmp/gtf2sam_fileRi3ZVm
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/cuffmerge_withkk/new/tmp/gtf2sam_fileLryIir
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/cuffmerge_withkk/new/tmp/gtf2sam_fileD7Hu7I
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/cuffmerge_withkk/new/tmp/gtf2sam_file6HoxTf
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/cuffmerge_withkk/new/tmp/gtf2sam_fileSWSGx1
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/cuffmerge_withkk/new/tmp/gtf2sam_fileOGgAW1
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/cuffmerge_withkk/new/tmp/gtf2sam_filezWVnJg
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/cuffmerge_withkk/new/tmp/gtf2sam_filek5fSwI
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/cuffmerge_withkk/new/tmp/gtf2sam_fileUe3cQo
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/cuffmerge_withkk/new/tmp/gtf2sam_fileIqqX1j
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/cuffmerge_withkk/new/tmp/gtf2sam_fileHLovet
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/cuffmerge_withkk/new/tmp/gtf2sam_fileD5SipP
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/cuffmerge_withkk/new/tmp/gtf2sam_fileznvWqq
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/cuffmerge_withkk/new/tmp/gtf2sam_fileTGUGLf
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/cuffmerge_withkk/new/tmp/gtf2sam_filenH2Tei
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/cuffmerge_withkk/new/tmp/gtf2sam_filenNNxPy
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/cuffmerge_withkk/new/tmp/gtf2sam_fileYLBrx2
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/cuffmerge_withkk/new/tmp/gtf2sam_fileJjG7kK
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/cuffmerge_withkk/new/tmp/gtf2sam_file4R2rlG
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/cuffmerge_withkk/new/tmp/gtf2sam_file8zvNZU
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/cuffmerge_withkk/new/tmp/gtf2sam_filemG8Fen
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/cuffmerge_withkk/new/tmp/gtf2sam_filesLDr92
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/cuffmerge_withkk/new/tmp/gtf2sam_fileO0se5V
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/cuffmerge_withkk/new/tmp/gtf2sam_fileIJevQ4
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/cuffmerge_withkk/new/tmp/gtf2sam_fileTVcvcv
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/cuffmerge_withkk/new/tmp/gtf2sam_file1nDasb
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/cuffmerge_withkk/new/tmp/gtf2sam_file6Gx3D9
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/cuffmerge_withkk/new/tmp/gtf2sam_file2OX9zn
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/cuffmerge_withkk/new/tmp/gtf2sam_filecTm9rR
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/cuffmerge_withkk/new/tmp/gtf2sam_filedOsGaB
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/cuffmerge_withkk/new/tmp/gtf2sam_file0W1F1A
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/cuffmerge_withkk/new/tmp/gtf2sam_fileyR89JQ
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/cuffmerge_withkk/new/tmp/gtf2sam_fileqaeJ3l
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/cuffmerge_withkk/new/tmp/gtf2sam_file2zaLE7
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/cuffmerge_withkk/new/tmp/gtf2sam_file9LuZGa
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/cuffmerge_withkk/new/tmp/gtf2sam_filewdTsIt
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/cuffmerge_withkk/new/tmp/gtf2sam_filesgn5J2
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/cuffmerge_withkk/new/tmp/gtf2sam_filezQfh9R
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/cuffmerge_withkk/new/tmp/gtf2sam_fileTGarzX
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/cuffmerge_withkk/new/tmp/gtf2sam_filewewHRi
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/cuffmerge_withkk/new/tmp/gtf2sam_fileGQaDWV
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/cuffmerge_withkk/new/tmp/gtf2sam_fileHruMaP
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/cuffmerge_withkk/new/tmp/gtf2sam_file9NzIcY
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/cuffmerge_withkk/new/tmp/gtf2sam_fileFJEVxo
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/cuffmerge_withkk/new/tmp/gtf2sam_file0jtis5
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/cuffmerge_withkk/new/tmp/gtf2sam_filepw0oz2
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/cuffmerge_withkk/new/tmp/gtf2sam_filerCNvGf
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/cuffmerge_withkk/new/tmp/gtf2sam_fileJgNNRI
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/cuffmerge_withkk/new/tmp/gtf2sam_file2rFwXr
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/cuffmerge_withkk/new/tmp/gtf2sam_fileAx7wGr
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/cuffmerge_withkk/new/tmp/gtf2sam_file5TeIoH
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/cuffmerge_withkk/new/tmp/gtf2sam_fileizm7Zc
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/cuffmerge_withkk/new/tmp/gtf2sam_fileHGLgs0
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/cuffmerge_withkk/new/tmp/gtf2sam_filegBkmB4
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/cuffmerge_withkk/new/tmp/gtf2sam_file7yNCnF
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/cuffmerge_withkk/new/tmp/gtf2sam_filevhE8Uw
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/cuffmerge_withkk/new/tmp/gtf2sam_filerknjwE
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/cuffmerge_withkk/new/tmp/gtf2sam_fileLItTG3
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/cuffmerge_withkk/new/tmp/gtf2sam_file6bnJBI
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/cuffmerge_withkk/new/tmp/gtf2sam_fileW9EcgD
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/cuffmerge_withkk/new/tmp/gtf2sam_filec7QDCN
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/cuffmerge_withkk/new/tmp/gtf2sam_filecrZEWd
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/cuffmerge_withkk/new/tmp/gtf2sam_fileQDrIpU
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/cuffmerge_withkk/new/tmp/gtf2sam_fileY3mTlS
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/cuffmerge_withkk/new/tmp/gtf2sam_filepqAWI4
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/cuffmerge_withkk/new/tmp/gtf2sam_fileHBl2Ev
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/cuffmerge_withkk/new/tmp/gtf2sam_fileNB1LRc
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/cuffmerge_withkk/new/tmp/gtf2sam_fileaL5vz9
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/cuffmerge_withkk/new/tmp/gtf2sam_file5w8cNk
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/cuffmerge_withkk/new/tmp/gtf2sam_fileuBSGNJ
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/cuffmerge_withkk/new/tmp/gtf2sam_file82lX5m
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/cuffmerge_withkk/new/tmp/gtf2sam_filelstWJe
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/cuffmerge_withkk/new/tmp/gtf2sam_fileWEKRpj
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/cuffmerge_withkk/new/tmp/gtf2sam_filebPUxsB
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/cuffmerge_withkk/new/tmp/gtf2sam_fileHMYED6
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/cuffmerge_withkk/new/tmp/gtf2sam_fileR5JRcP
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/cuffmerge_withkk/new/tmp/gtf2sam_fileyxMKOL
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/cuffmerge_withkk/new/tmp/gtf2sam_filefqiBpV
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/cuffmerge_withkk/new/tmp/gtf2sam_file52zosi
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/cuffmerge_withkk/new/tmp/gtf2sam_fileCMIsyS
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/cuffmerge_withkk/new/tmp/gtf2sam_fileyuNvYF
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/cuffmerge_withkk/new/tmp/gtf2sam_fileZSHJDG
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/cuffmerge_withkk/new/tmp/gtf2sam_fileKKRcgW
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/cuffmerge_withkk/new/tmp/gtf2sam_file1CkP3o
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/cuffmerge_withkk/new/tmp/gtf2sam_fileGNqXV9
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/cuffmerge_withkk/new/tmp/gtf2sam_fileHQi0Da
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/cuffmerge_withkk/new/tmp/gtf2sam_fileyCE2Cr
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/cuffmerge_withkk/new/tmp/gtf2sam_fileNHyECY
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/cuffmerge_withkk/new/tmp/gtf2sam_fileQFyCWL
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/cuffmerge_withkk/new/tmp/gtf2sam_filerG2nFP
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/cuffmerge_withkk/new/tmp/gtf2sam_file5FRYz9
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/AL-ZT10-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileQTk2cK
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/AL-ZT10-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file5evi5y
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/AL-ZT14-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileVKCcXB
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/AL-ZT14-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileSTT3uS
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/AL-ZT18-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filek6NBPm
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/AL-ZT18-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filedUTFq4
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/AL-ZT2-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filemwXB7Z
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/AL-ZT2-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileOvWU8b
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/AL-ZT22-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filepTJL3C
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/AL-ZT22-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileA6LUOh
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/AL-ZT6-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileanz6fa
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/AL-ZT6-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileiOQVDg
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CR-ZT10-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filemfkJ3z
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CR-ZT10-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filejVzaZ8
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CR-ZT14-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileorSh9V
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CR-ZT14-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileDhs8kY
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CR-ZT18-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file5vdApe
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CR-ZT18-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileNvXYfI
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CR-ZT2-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filewN3Lsr
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CR-ZT2-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file3By8Oo
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CRZT22-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileVhx3MB
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CR-ZT22-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filehFAPC3
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CR-ZT6-1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileUyinRK
gtf_to_sam -F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/CR-ZT6-2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileQS5wwF
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/CV_BDE47_1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file2VAQvN
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/CV_BDE47_2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileGhjrEb
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/CV_BDE47_3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileafJtgO
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/CV_BDE47_4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileFzRbrF
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/CV_BDE99_1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileBYeW7K
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/CV_BDE99_2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileWE2Hd6
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/CV_CO1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileWFu5FF
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/CV_CO2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileXavK4u
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/CV_CO3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file7URJaA
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/GF_BDE47_1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileWuxfIT
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/GF_BDE47_2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filePZ9jLt
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/GF_BDE47_3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileF8LVhi
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/GF_BDE99_1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileRRB00m
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/GF_BDE99_2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filexi7jBJ
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/GF_BDE99_3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file0ZzF1m
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/GF_CO1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filep5n6bg
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/GF_CO2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file3AqXup
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/GF_CO3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filexzMRrM
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/Cyp2bnull_HFD_M1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileP9RcCo
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/Cyp2bnull_HFD_M2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileApijuh
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/Cyp2bnull_HFD_M3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filenjmoKs
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/Cyp2bnull_ND_M1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filePJMbHT
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/Cyp2bnull_ND_M2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileIqG6oC
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/Cyp2bnull_ND_M3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filekIj2kB
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT_HFD_M1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileB8sX0Q
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT_HFD_M2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileiY8rCn
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT_HFD_M3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filewFSaI9
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT_ND_M1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filedtiXUc
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT_ND_M2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileetzv6x
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT_ND_M3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileS87mx9
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/16wk_ASNase1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileIBevU0
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/16wk_ASNase2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileAkHIR8
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/16wk_ASNase3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file5GVrDw
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/16wk_PBS1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filer1cZea
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/16wk_PBS2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file828cK3
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/16wk_PBS3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileY1Ybld
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/2wk_ASNase1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file0eXDxC
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/2wk_ASNase2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileUXdxDh
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/2wk_ASNase3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filerSTwVc
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/2wk_PBS1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileGjxHMo
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/2wk_PBS2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filerCcSGQ
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/2wk_PBS3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filemCvyyy
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/8wk_ASNase1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileN1A1Nx
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/8wk_ASNase2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileT9J4DM
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/8wk_ASNase3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileP4r3ch
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/8wk_PBS1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filehoLth1
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/8wk_PBS2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileh9V7w0
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/8wk_PBS3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file33jo2e
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/PB1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filevhihDJ
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/PB2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileGzLzdr
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/PB_LivTum1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileMWPCll
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/PB_LivTum2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileyPOA9r
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/PB_LivTum3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileQ2jp9M
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileCdbhkl
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filepgTgg6
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/KI1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileZ2BeL3
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/KI2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file1qlrjg
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/KI3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileW9RQiG
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/KI4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filejkWSIj
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/KI5_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileJct72a
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/KI6_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileuCBDEg
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/KI7_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileIwNDOz
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/KI8_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filebi4EL6
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/KI9_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileQQo6qR
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/KI10_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileI16bkP
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/KI11_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file5N07I0
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/KI12_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file53wgnq
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filetx45A3
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileWTD1ZT
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileOF7xGY
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileXPoNSg
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT5_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileYcDePM
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT6_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileqe8ebw
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT7_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileCZ735t
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT8_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filednlU6F
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT9_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file2vWJA5
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT10_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileriiDAI
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT11_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileQjfXHz
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/WT12_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileRYPjZE
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/ERaflox_F_Met1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file1LpvRX
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/ERaflox_F_Met2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filekzD1ov
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/ERaflox_F_Met3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileh47xXh
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/ERaflox_F_Met4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileZLbSlj
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/ERaflox_F_Pro1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file99qhCz
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/ERaflox_F_Pro2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filesYZVM5
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/ERaflox_F_Pro3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filecSwgYS
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/ERaflox_F_Pro4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileUVSdHV
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/ERaflox_male1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filejTy8yd
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/ERaflox_male2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filexABN8J
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/ERaflox_male3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileL4mmVv
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/ERaflox_male4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileg2pxGw
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/LERKO_male1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileQO9ZfN
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/LERKO_male2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file8VOLsk
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/LERKO_male3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileUloWp6
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/LERKO_male4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filev8ZDB7
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/LERKOflox_F_Met1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileSA0Ako
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/LERKOflox_F_Met2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filepp8dkU
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/LERKOflox_F_Met3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file0SksmF
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/LERKOflox_F_Met4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileXVvzBF
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/LERKOflox_F_Pro1_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileFFzwHU
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/LERKOflox_F_Pro2_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file7c62Yo
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/LERKOflox_F_Pro3_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileGb4AP8
gtf_to_sam -F /restricted/projectnb/waxmanlab/varsha/cufflinks/LERKOflox_F_Pro4_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileiUPmM7
sort -k 3,3 -k 4,4n --temporary-directory=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filexa3lOU /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileWitpKT /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileHZ5Fe8 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileMSIOFF /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileBNS8lu /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filePZ4YMy /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file6GF48T /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileEvw8ox /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileMiodRq /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filegLtnXz /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file8wXVVY /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileyYrlTD /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileuxEB9z /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file6hm63L /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file9cSQEd /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileJICyOU /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileZsiNzR /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file0iA3I2 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file2N18vr /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileNCIbk4 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filekhrD7T /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filexRXstX /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileLHbPJe /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filekp61EJ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileTIoLYr /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileMLhXmo /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileWIVFfy /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileeQaDaW /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileJ2yiSx /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileQm1Y4o /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileFfhWEv /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filehyzQ2P /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filegtQvRp /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileZnVwid /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filedBpUue /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file8zjBmt /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileZqV4TV /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filez5RiOB /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file0tIZ8u /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileZcFw8B /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filePvxCKW /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileJWdGBu /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileQGmf2f /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileKjVaFe /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileHS6Srq /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filerqklwP /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filea2TVyr /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filexDJzPg /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filewulKCj /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileWGQdaA /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filendGE35 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileM2G3XQ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileFj0DFQ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filehegHr5 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileZxu5fz /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileOaRYIj /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file3O6Mbj /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file9Tk1xx /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file0m5yH0 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileXVMgAK /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file0QYlzJ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filetsN8GX /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileJoCwUq /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileMqCFJa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileIhpjt9 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file32s9ln /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileAqRlqQ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileY0Nupy /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filefvy7Gv /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filef0rdQH /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file1mOJR8 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileeh4PwP /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filehFibGL /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filefsPXhX /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileykU8Sl /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file1UQgvY /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileUwsnHP /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_files1SiDT /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filexdtogb /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileThIrUG /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileiMuyFq /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileKTL1bo /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filev7ZuOy /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filepIR9tW /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file7et02x /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileRi3ZVm /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileLryIir /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileD7Hu7I /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file6HoxTf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileSWSGx1 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileOGgAW1 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filezWVnJg /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filek5fSwI /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileUe3cQo /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileIqqX1j /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileHLovet /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileD5SipP /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileznvWqq /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileTGUGLf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filenH2Tei /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filenNNxPy /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileYLBrx2 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileJjG7kK 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/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file33jo2e /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filevhihDJ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileGzLzdr /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileMWPCll /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileyPOA9r /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileQ2jp9M /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileCdbhkl /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filepgTgg6 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileZ2BeL3 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file1qlrjg /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileW9RQiG /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filejkWSIj /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileJct72a /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileuCBDEg /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileIwNDOz /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filebi4EL6 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileQQo6qR /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileI16bkP /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file5N07I0 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file53wgnq /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filetx45A3 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileWTD1ZT /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileOF7xGY /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileXPoNSg /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileYcDePM /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileqe8ebw /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileCZ735t /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filednlU6F /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file2vWJA5 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileriiDAI /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileQjfXHz /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileRYPjZE /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file1LpvRX /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filekzD1ov /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileh47xXh /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileZLbSlj /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file99qhCz /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filesYZVM5 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filecSwgYS /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileUVSdHV /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filejTy8yd /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filexABN8J /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileL4mmVv /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileg2pxGw /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileQO9ZfN /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file8VOLsk /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileUloWp6 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filev8ZDB7 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileSA0Ako /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_filepp8dkU /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file0SksmF /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileXVvzBF /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileFFzwHU /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_file7c62Yo /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileGb4AP8 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/gtf2sam_fileiUPmM7 > /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/tmp/mergeSam_fileL4XIYl
cufflinks -o /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/ -F 0.05 -g /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/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/cuffmerge_withkk/new/tmp/mergeSam_fileL4XIYl
cuffcompare -o tmp_meta_asm -C -G  -r /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/genes.gtf  -s /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/genomeWithRandom.fa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new//transcripts.gtf
cuffcompare -o tmp_meta_asm -C -G  -r /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/genes.gtf  -s /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new/genomeWithRandom.fa /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_withkk/new//merged.gtf