/share/pkg.7/cufflinks/2.2.1/install/bin/cuffmerge -o /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all -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-0001_cufflinks/transcripts.gtf /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filelQQTwY
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_all/tmp/gtf2sam_fileOkOYeW
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_all/tmp/gtf2sam_filesZwX9b
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_all/tmp/gtf2sam_filegb5QYI
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_all/tmp/gtf2sam_fileElteiv
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_all/tmp/gtf2sam_filecH0t6x
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_all/tmp/gtf2sam_fileP8JdES
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_all/tmp/gtf2sam_fileES2ldt
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_all/tmp/gtf2sam_filexob0Gj
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_all/tmp/gtf2sam_file77f49p
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_all/tmp/gtf2sam_filebE9cUM
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_all/tmp/gtf2sam_filePNpSyp
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_all/tmp/gtf2sam_filebGJjgi
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_all/tmp/gtf2sam_filehHDKQq
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_all/tmp/gtf2sam_file3qwRYO
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_all/tmp/gtf2sam_filen0MAgt
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_all/tmp/gtf2sam_file15JRul
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_all/tmp/gtf2sam_fileKbHl2r
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_all/tmp/gtf2sam_fileaQYoFM
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_all/tmp/gtf2sam_fileFX47wk
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_all/tmp/gtf2sam_file2mGiQ5
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_all/tmp/gtf2sam_fileiZWD85
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_all/tmp/gtf2sam_fileVCw8yk
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_all/tmp/gtf2sam_fileVJmFAM
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_all/tmp/gtf2sam_file3PNIFs
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_all/tmp/gtf2sam_fileXaUQhm
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_all/tmp/gtf2sam_file5BpmIt
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_all/tmp/gtf2sam_fileqevhTO
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_all/tmp/gtf2sam_file3UXI5n
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_all/tmp/gtf2sam_filei5WXzb
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_all/tmp/gtf2sam_filekMcwbd
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_all/tmp/gtf2sam_fileELR14s
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_all/tmp/gtf2sam_filewSZOQW
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_all/tmp/gtf2sam_fileHnrMsE
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_all/tmp/gtf2sam_file95Yhaz
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_all/tmp/gtf2sam_fileVzh9MG
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_all/tmp/gtf2sam_fileW6LMV1
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_all/tmp/gtf2sam_fileby0N5A
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_all/tmp/gtf2sam_fileRDhQGo
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_all/tmp/gtf2sam_filek4j1Bp
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_all/tmp/gtf2sam_fileyIlBbE
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_all/tmp/gtf2sam_fileJM2H25
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_all/tmp/gtf2sam_fileGLqUeL
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_all/tmp/gtf2sam_filezgSDSD
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_all/tmp/gtf2sam_fileJdaOoK
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_all/tmp/gtf2sam_filenz1qb4
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_all/tmp/gtf2sam_file4VgaPB
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_all/tmp/gtf2sam_filerko38m
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_all/tmp/gtf2sam_fileV5bZCm
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_all/tmp/gtf2sam_fileQ5K3jB
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_all/tmp/gtf2sam_fileaBZw84
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_all/tmp/gtf2sam_file8D3t9N
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_all/tmp/gtf2sam_filerFfZyM
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_all/tmp/gtf2sam_file7XsRw0
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_all/tmp/gtf2sam_filegAILNt
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_all/tmp/gtf2sam_file7IrnBc
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_all/tmp/gtf2sam_fileKPAyxa
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_all/tmp/gtf2sam_fileu5Gjsn
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_all/tmp/gtf2sam_filekaCCLP
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_all/tmp/gtf2sam_filekJpU3w
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_all/tmp/gtf2sam_file5GvFKu
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_all/tmp/gtf2sam_fileGw07UH
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_all/tmp/gtf2sam_filejIkGaa
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_all/tmp/gtf2sam_file3kno8Q
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_all/tmp/gtf2sam_filejQiNWN
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_all/tmp/gtf2sam_file4xWdYZ
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_all/tmp/gtf2sam_filepF6wir
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_all/tmp/gtf2sam_fileMhp3Z7
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_all/tmp/gtf2sam_fileofxVd4
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_all/tmp/gtf2sam_fileCOypgf
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_all/tmp/gtf2sam_fileJInZxF
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_all/tmp/gtf2sam_file2Fuo8k
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_all/tmp/gtf2sam_fileLBdCGf
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_all/tmp/gtf2sam_fileWAX8Km
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_all/tmp/gtf2sam_filehy7DdI
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_all/tmp/gtf2sam_fileeRmxbh
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_all/tmp/gtf2sam_file5q7Bw3
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_all/tmp/gtf2sam_filerOUXK2
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_all/tmp/gtf2sam_fileEzC4sf
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_all/tmp/gtf2sam_file2ZixaF
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_all/tmp/gtf2sam_fileiQDPdi
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_all/tmp/gtf2sam_filev3YFf8
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_all/tmp/gtf2sam_fileCBIohb
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_all/tmp/gtf2sam_fileix10gs
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_all/tmp/gtf2sam_fileDAJO3W
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_all/tmp/gtf2sam_fileIVd2aG
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_all/tmp/gtf2sam_filefVflFC
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_all/tmp/gtf2sam_file82hyxN
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_all/tmp/gtf2sam_filerjfsxb
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_all/tmp/gtf2sam_fileitm7ZM
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_all/tmp/gtf2sam_fileR7clbB
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_all/tmp/gtf2sam_filelRx6nC
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_all/tmp/gtf2sam_fileF3cRfQ
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_all/tmp/gtf2sam_fileAN7FFi
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_all/tmp/gtf2sam_file9WQD7Y
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_all/tmp/gtf2sam_file6wBxRS
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_all/tmp/gtf2sam_filef1l1n1
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_all/tmp/gtf2sam_fileFX5kPn
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_all/tmp/gtf2sam_fileJwM5rX
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_all/tmp/gtf2sam_fileKIH0uL
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_all/tmp/gtf2sam_fileBTPeHM
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_all/tmp/gtf2sam_fileeDWof1
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_all/tmp/gtf2sam_fileHYy7Qs
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_all/tmp/gtf2sam_file58tsV8
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_all/tmp/gtf2sam_fileqzDMo2
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_all/tmp/gtf2sam_filerM7rYa
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_all/tmp/gtf2sam_file9U28zw
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_all/tmp/gtf2sam_fileSf1Dn8
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_all/tmp/gtf2sam_filewtkZNZ
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_all/tmp/gtf2sam_filedDcMw7
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_all/tmp/gtf2sam_fileGeIzsv
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_all/tmp/gtf2sam_file4dEFa9
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_all/tmp/gtf2sam_fileqrSuq4
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_all/tmp/gtf2sam_fileIZAjBf
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_all/tmp/gtf2sam_filesQAQ2G
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_all/tmp/gtf2sam_fileop7ACo
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_all/tmp/gtf2sam_fileSwteSn
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_all/tmp/gtf2sam_filegniRBD
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_all/tmp/gtf2sam_filemEeEd9
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_all/tmp/gtf2sam_filelpOWTU
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_all/tmp/gtf2sam_fileKzcVUW
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_all/tmp/gtf2sam_file3l1eXd
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_all/tmp/gtf2sam_fileE1c0KK
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_all/tmp/gtf2sam_filebUN1xx
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_all/tmp/gtf2sam_fileFTntsA
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_all/tmp/gtf2sam_filebZekwT
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_all/tmp/gtf2sam_fileXd7Jxs
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_all/tmp/gtf2sam_fileXnRCSh
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_all/tmp/gtf2sam_fileaGqHhn
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_all/tmp/gtf2sam_filePcHb2I
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_all/tmp/gtf2sam_fileIdtBik
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_all/tmp/gtf2sam_fileJh7rvb
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_all/tmp/gtf2sam_filecB3Yli
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_all/tmp/gtf2sam_fileXRRjSE
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_all/tmp/gtf2sam_fileqXo5yh
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_all/tmp/gtf2sam_filew0H3ta
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_all/tmp/gtf2sam_fileH3mnCj
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_all/tmp/gtf2sam_fileP7Lt1I
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_all/tmp/gtf2sam_filezhtxTo
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_all/tmp/gtf2sam_filePYHDKk
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_all/tmp/gtf2sam_filepSJ7Yw
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_all/tmp/gtf2sam_fileOiAFxZ
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_all/tmp/gtf2sam_fileS0PeYH
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_all/tmp/gtf2sam_fileMQmtrG
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_all/tmp/gtf2sam_file4VZP8U
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_all/tmp/gtf2sam_files6Rutr
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_all/tmp/gtf2sam_file0JPvAf
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_all/tmp/gtf2sam_fileyPCM0j
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_all/tmp/gtf2sam_filejN1HZC
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_all/tmp/gtf2sam_filex6pkAa
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_all/tmp/gtf2sam_filey0BATW
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_all/tmp/gtf2sam_filetztCyX
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_all/tmp/gtf2sam_fileSfXbqc
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_all/tmp/gtf2sam_filemyZiyF
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_all/tmp/gtf2sam_filev6RkHm
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_all/tmp/gtf2sam_file7J8swi
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_all/tmp/gtf2sam_fileXMy93q
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_all/tmp/gtf2sam_file7CaQqM
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_all/tmp/gtf2sam_filedXSWll
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_all/tmp/gtf2sam_filewGtiJ7
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_all/tmp/gtf2sam_filemS7z17
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_all/tmp/gtf2sam_fileMmUbtl
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_all/tmp/gtf2sam_fileJPz4aM
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_all/tmp/gtf2sam_file4wuAIr
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_all/tmp/gtf2sam_file6fbKpk
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_all/tmp/gtf2sam_filevAEfzq
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_all/tmp/gtf2sam_fileLy6CxK
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_all/tmp/gtf2sam_fileBWXN1h
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_all/tmp/gtf2sam_fileYsfcT5
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_all/tmp/gtf2sam_filetgne39
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_all/tmp/gtf2sam_fileWatlEu
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_all/tmp/gtf2sam_fileKUX2r5
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_all/tmp/gtf2sam_file1WIAKW
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_all/tmp/gtf2sam_filep8HRl4
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_all/tmp/gtf2sam_filesik9ns
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_all/tmp/gtf2sam_file6de6h7
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_all/tmp/gtf2sam_file9X8SM0
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_all/tmp/gtf2sam_fileEUaRJ8
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_all/tmp/gtf2sam_file15OePu
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_all/tmp/gtf2sam_filepxpGg4
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_all/tmp/gtf2sam_file0cOf4Q
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_all/tmp/gtf2sam_filemN4WlS
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_all/tmp/gtf2sam_fileXkwyv8
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_all/tmp/gtf2sam_file3tD4oD
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_all/tmp/gtf2sam_file8xwYkl
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_all/tmp/gtf2sam_fileZkuhah
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_all/tmp/gtf2sam_fileFaavjq
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_all/tmp/gtf2sam_fileYDLW6L
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_all/tmp/gtf2sam_filea07apm
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_all/tmp/gtf2sam_fileMmwDya
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_all/tmp/gtf2sam_fileNVyiNb
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_all/tmp/gtf2sam_fileeYJGEp
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_all/tmp/gtf2sam_file2HEuGQ
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_all/tmp/gtf2sam_fileKm9NKw
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_all/tmp/gtf2sam_filefATYXp
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_all/tmp/gtf2sam_fileoRkgQw
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_all/tmp/gtf2sam_fileyaO1fT
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_all/tmp/gtf2sam_filebXxbyt
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_all/tmp/gtf2sam_fileGbhXIg
sort -k 3,3 -k 4,4n --temporary-directory=/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filelQQTwY /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileOkOYeW /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filesZwX9b /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filegb5QYI /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileElteiv /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filecH0t6x /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileP8JdES /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileES2ldt 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/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileSfXbqc /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filemyZiyF /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filev6RkHm /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_file7J8swi /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileXMy93q /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_file7CaQqM /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filedXSWll /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filewGtiJ7 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filemS7z17 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileMmUbtl /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileJPz4aM /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_file4wuAIr /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_file6fbKpk /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filevAEfzq /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileLy6CxK /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileBWXN1h /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileYsfcT5 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filetgne39 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileWatlEu /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileKUX2r5 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_file1WIAKW /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filep8HRl4 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filesik9ns /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_file6de6h7 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_file9X8SM0 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileEUaRJ8 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_file15OePu /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filepxpGg4 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_file0cOf4Q /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filemN4WlS /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileXkwyv8 /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_file3tD4oD /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_file8xwYkl /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileZkuhah /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileFaavjq /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileYDLW6L /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filea07apm /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileMmwDya /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileNVyiNb /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileeYJGEp /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_file2HEuGQ /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileKm9NKw /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filefATYXp /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileoRkgQw /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileyaO1fT /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_filebXxbyt /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/gtf2sam_fileGbhXIg > /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/tmp/mergeSam_fileMbdoJg
cufflinks -o /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/cufflinks/cuffmerge_all/ -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/cuffmerge_all/tmp/mergeSam_fileMbdoJg
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/cuffmerge_all//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/cuffmerge_all//merged.gtf