/N/dc2/projects/marinovg/programs/cufflinks-2.2.0.Linux_x86_64/cuffmerge -p 16 -o cuffmerge-2.2.0-Paramecium_sexaurelia --ref-gtf /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf Paramecium_sexaurelia.assembly_list.txt
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium-sexaurelia/Paramecium-sexaurelia-Sample_6D1-2x100-TopHat-2.0.8-minIntron10-more-reads/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_sexaurelia/tmp/gtf2sam_fileYyjx5A
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium-sexaurelia/Paramecium-sexaurelia-Sample_6D2-2x100-TopHat-2.0.8-minIntron10-more-reads/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_sexaurelia/tmp/gtf2sam_fileQ3KH71
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium-sexaurelia/Paramecium-sexaurelia-Sample_6V-2x100-TopHat-2.0.8-minIntron10-more-reads/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_sexaurelia/tmp/gtf2sam_fileN4vJrw
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium-sexaurelia/Paramecium-sexaurelia-strain_CA1-autogamy-141105-sex-2x100-TopHat-2.0.8-minIntron10/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_sexaurelia/tmp/gtf2sam_file2ih453
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium-sexaurelia/Paramecium-sexaurelia-strain_CA1-vegetative-110506_IRIS_00020-para3-2x100-TopHat-2.0.8-minIntron10/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_sexaurelia/tmp/gtf2sam_file3SAYKC
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium-sexaurelia/Paramecium-sexaurelia-strain_CA1-vegetative-141105-6V-2x100-TopHat-2.0.8-minIntron10/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_sexaurelia/tmp/gtf2sam_file85dN8g
sort -k 3,3 -k 4,4n --temporary-directory=cuffmerge-2.2.0-Paramecium_sexaurelia/tmp/ cuffmerge-2.2.0-Paramecium_sexaurelia/tmp/gtf2sam_fileYyjx5A cuffmerge-2.2.0-Paramecium_sexaurelia/tmp/gtf2sam_fileQ3KH71 cuffmerge-2.2.0-Paramecium_sexaurelia/tmp/gtf2sam_fileN4vJrw cuffmerge-2.2.0-Paramecium_sexaurelia/tmp/gtf2sam_file2ih453 cuffmerge-2.2.0-Paramecium_sexaurelia/tmp/gtf2sam_file3SAYKC cuffmerge-2.2.0-Paramecium_sexaurelia/tmp/gtf2sam_file85dN8g > cuffmerge-2.2.0-Paramecium_sexaurelia/tmp/mergeSam_fileDugdbX
cufflinks -o cuffmerge-2.2.0-Paramecium_sexaurelia/ -F 0.05 -g /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_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_sexaurelia/tmp/mergeSam_fileDugdbX
cuffcompare -o tmp_meta_asm -C -G  -r /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf  cuffmerge-2.2.0-Paramecium_sexaurelia//transcripts.gtf
cuffcompare -o tmp_meta_asm -C -G  -r /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_sexaurelia_AZ8-4/sexaurelia_AZ8-4_annotation_v1.gtf  cuffmerge-2.2.0-Paramecium_sexaurelia//merged.gtf