/N/dc2/projects/marinovg/programs/cufflinks-2.2.0.Linux_x86_64/cuffmerge -p 16 -o cuffmerge-2.2.0-Paramecium_primaurelia --ref-gtf /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf Paramecium_primaurelia.assembly_list.txt
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium_primaurelia/Paramecium_primaurelia-Sample_1D1-2x100-TopHat-2.0.8-minIntron10-more-reads/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_primaurelia/tmp/gtf2sam_file3XhxG9
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium_primaurelia/Paramecium_primaurelia-Sample_1D2-2x100-TopHat-2.0.8-minIntron10-more-reads/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_primaurelia/tmp/gtf2sam_fileUm4Eow
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium_primaurelia/Paramecium_primaurelia-Sample_1V-2x100-TopHat-2.0.8-minIntron10-more-reads/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_primaurelia/tmp/gtf2sam_fileZhuxrW
sort -k 3,3 -k 4,4n --temporary-directory=cuffmerge-2.2.0-Paramecium_primaurelia/tmp/ cuffmerge-2.2.0-Paramecium_primaurelia/tmp/gtf2sam_file3XhxG9 cuffmerge-2.2.0-Paramecium_primaurelia/tmp/gtf2sam_fileUm4Eow cuffmerge-2.2.0-Paramecium_primaurelia/tmp/gtf2sam_fileZhuxrW > cuffmerge-2.2.0-Paramecium_primaurelia/tmp/mergeSam_fileHWEuEn
cufflinks -o cuffmerge-2.2.0-Paramecium_primaurelia/ -F 0.05 -g /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 16 cuffmerge-2.2.0-Paramecium_primaurelia/tmp/mergeSam_fileHWEuEn
cuffcompare -o tmp_meta_asm -C -G  -r /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf  cuffmerge-2.2.0-Paramecium_primaurelia//transcripts.gtf
cuffcompare -o tmp_meta_asm -C -G  -r /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_primaurelia_Ir4-2/primaurelia_Ir4-2_annotation_v1.gtf  cuffmerge-2.2.0-Paramecium_primaurelia//merged.gtf