/usr/local2/cufflinks-2.1.1.Linux_x86_64//cuffmerge -o cuffmerge_out -g Crassostrea_gigas.GCA_000297895.1.21.gtf -s Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel.fa --min-isoform-fraction 0.1 gtf_to_merge.txt
gtf_to_sam -F T1_transcripts.gtf cuffmerge_out/tmp/gtf2sam_fileihdNzn
gtf_to_sam -F T2_transcripts.gtf cuffmerge_out/tmp/gtf2sam_file9QsDLN
gtf_to_sam -F U1_transcripts.gtf cuffmerge_out/tmp/gtf2sam_fileU4N4ek
gtf_to_sam -F U2_transcripts.gtf cuffmerge_out/tmp/gtf2sam_fileXPnNE0
sort -k 3,3 -k 4,4n --temporary-directory=cuffmerge_out/tmp/ cuffmerge_out/tmp/gtf2sam_fileihdNzn cuffmerge_out/tmp/gtf2sam_file9QsDLN cuffmerge_out/tmp/gtf2sam_fileU4N4ek cuffmerge_out/tmp/gtf2sam_fileXPnNE0 > cuffmerge_out/tmp/mergeSam_fileWErbbR
cufflinks -o cuffmerge_out/ -F 0.1 -g Crassostrea_gigas.GCA_000297895.1.21.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 1 cuffmerge_out/tmp/mergeSam_fileWErbbR
cuffcompare -o tmp_meta_asm -C -G  -r Crassostrea_gigas.GCA_000297895.1.21.gtf  -s Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel.fa cuffmerge_out//transcripts.gtf
cuffcompare -o tmp_meta_asm -C -G  -r Crassostrea_gigas.GCA_000297895.1.21.gtf  -s Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel.fa cuffmerge_out//merged.gtf