/usr/local2/cufflinks-2.1.1.Linux_x86_64//cuffmerge -o cuffmerge_out -g Crassostrea_gigas.GCA_000297895.1.24.gtf -s Crassostrea_gigas.GCA_000297895.1.24.dna_sm.toplevel.fa --min-isoform-fraction 0.1 gtf_to_merge.txt
gtf_to_sam -F 2M_AGTCAA_L001_R1_001_transcripts.gtf cuffmerge_out/tmp/gtf2sam_fileLcVCvY
gtf_to_sam -F 2M-HS_CCGTCC_L001_R1_001_transcripts.gtf cuffmerge_out/tmp/gtf2sam_fileAaXS2B
gtf_to_sam -F 4M_AGTTCC_L001_R1_001_transcripts.gtf cuffmerge_out/tmp/gtf2sam_file8EqxAs
gtf_to_sam -F 4M-HS_GTCCGC_L001_R1_001_transcripts.gtf cuffmerge_out/tmp/gtf2sam_fileuNytzw
gtf_to_sam -F 6M_ATGTCA_L001_R1_001_transcripts.gtf cuffmerge_out/tmp/gtf2sam_fileEcIsPL
gtf_to_sam -F 6M-HS_GTGAAA_L001_R1_001_transcripts.gtf cuffmerge_out/tmp/gtf2sam_fileSgzh5d
sort -k 3,3 -k 4,4n --temporary-directory=cuffmerge_out/tmp/ cuffmerge_out/tmp/gtf2sam_fileLcVCvY cuffmerge_out/tmp/gtf2sam_fileAaXS2B cuffmerge_out/tmp/gtf2sam_file8EqxAs cuffmerge_out/tmp/gtf2sam_fileuNytzw cuffmerge_out/tmp/gtf2sam_fileEcIsPL cuffmerge_out/tmp/gtf2sam_fileSgzh5d > cuffmerge_out/tmp/mergeSam_file8Xcx3Q
cufflinks -o cuffmerge_out/ -F 0.1 -g Crassostrea_gigas.GCA_000297895.1.24.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_file8Xcx3Q
cuffcompare -o tmp_meta_asm -C -G  -r Crassostrea_gigas.GCA_000297895.1.24.gtf  -s Crassostrea_gigas.GCA_000297895.1.24.dna_sm.toplevel.fa cuffmerge_out//transcripts.gtf
cuffcompare -o tmp_meta_asm -C -G  -r Crassostrea_gigas.GCA_000297895.1.24.gtf  -s Crassostrea_gigas.GCA_000297895.1.24.dna_sm.toplevel.fa cuffmerge_out//merged.gtf