/N/dc2/projects/marinovg/programs/cufflinks-2.2.0.Linux_x86_64/cuffmerge -p 16 -o cuffmerge-2.2.0-Paramecium_biaurelia --ref-gtf /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf Paramecium_biaurelia.assembly_list.txt
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium_biaurelia/Paramecium-biaurelia-Sample_2D1-2x100-TopHat-2.0.8-minIntron10-more-reads/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_file220rVt
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium_biaurelia/Paramecium-biaurelia-Sample_2D2-2x100-TopHat-2.0.8-minIntron10-more-reads/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_file7vvfKT
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium_biaurelia/Paramecium-biaurelia-Sample_2V-2x100-TopHat-2.0.8-minIntron10-more-reads/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_file5Lusxn
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium_biaurelia/Paramecium-biaurelia-Sample_bi-2x100-TopHat-2.0.8-minIntron10-more-reads/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_fileZwDufT
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium_biaurelia/Paramecium-biaurelia-strain_V1-4-autogamy-110506_IRIS_00020-2x100-TopHat-2.0.8-minIntron10/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_file9ysjas
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium_biaurelia/Paramecium-biaurelia-strain_V1-4-autogamy-141105-bi-2x100-TopHat-2.0.8-minIntron10/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_fileTNpOg5
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium_biaurelia/Paramecium-biaurelia-strain_V1-4-vegetative-110506_IRIS_00020-para1-2x100-TopHat-2.0.8-minIntron10/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_fileVB8KqI
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium_biaurelia/Paramecium-biaurelia-strain_V1-4-vegetative-141105-2V-2x100-TopHat-2.0.8-minIntron10/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_filezxz9qq
sort -k 3,3 -k 4,4n --temporary-directory=cuffmerge-2.2.0-Paramecium_biaurelia/tmp/ cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_file220rVt cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_file7vvfKT cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_file5Lusxn cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_fileZwDufT cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_file9ysjas cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_fileTNpOg5 cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_fileVB8KqI cuffmerge-2.2.0-Paramecium_biaurelia/tmp/gtf2sam_filezxz9qq > cuffmerge-2.2.0-Paramecium_biaurelia/tmp/mergeSam_fileMWyGDb
cufflinks -o cuffmerge-2.2.0-Paramecium_biaurelia/ -F 0.05 -g /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_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_biaurelia/tmp/mergeSam_fileMWyGDb
cuffcompare -o tmp_meta_asm -C -G  -r /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf  cuffmerge-2.2.0-Paramecium_biaurelia//transcripts.gtf
cuffcompare -o tmp_meta_asm -C -G  -r /N/dc2/projects/marinovg/genomes/Ciliates/Paramecium_biaurelia_V1-4/biaurelia_V1-4_annotation_v1.gtf  cuffmerge-2.2.0-Paramecium_biaurelia//merged.gtf