/N/dc2/projects/marinovg/programs/cufflinks-2.2.0.Linux_x86_64/cuffmerge -p 16 -o cuffmerge-2.2.0-Paramecium_tetraurelia-noref Paramecium_tetraurelia.assembly_list.txt
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium-tetraurelia/Paramecium-tetraurelia-strain_unknown_1-autogamy-141105-tet-2x100-TopHat-2.0.8-minIntron10/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/gtf2sam_filesQ6va7
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium-tetraurelia/Paramecium-tetraurelia-strain_unknown_1-vegetative-110506_IRIS_00020-para4-2x100-TopHat-2.0.8-minIntron10/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/gtf2sam_filepVKxKV
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium-tetraurelia/Paramecium-tetraurelia-strain_unknown_1-vegetative-141105-4V-2x100-TopHat-2.0.8-minIntron10/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/gtf2sam_fileUATOIN
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium-tetraurelia/Paramecium_tetraurelia-Sample_172-2x100-TopHat-2.0.8-minIntron10-more-reads/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/gtf2sam_fileyAgapI
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium-tetraurelia/Paramecium_tetraurelia-Sample_4D1-2x100-TopHat-2.0.8-minIntron10-more-reads/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/gtf2sam_filesT53QG
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium-tetraurelia/Paramecium_tetraurelia-Sample_4D2-2x100-TopHat-2.0.8-minIntron10-more-reads/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/gtf2sam_fileYj861H
gtf_to_sam -F /N/dc2/projects/marinovg/Paramecium/RNA-seq/Paramecium-tetraurelia/Paramecium_tetraurelia-Sample_4D_2_14_16_12-2x100-TopHat-2.0.8-minIntron10-more-reads/stringtie-1.0.3-de-novo.gtf cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/gtf2sam_fileTYXb1M
sort -k 3,3 -k 4,4n --temporary-directory=cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/ cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/gtf2sam_filesQ6va7 cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/gtf2sam_filepVKxKV cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/gtf2sam_fileUATOIN cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/gtf2sam_fileyAgapI cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/gtf2sam_filesT53QG cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/gtf2sam_fileYj861H cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/gtf2sam_fileTYXb1M > cuffmerge-2.2.0-Paramecium_tetraurelia-noref/tmp/mergeSam_fileyNrdmV
cufflinks -o cuffmerge-2.2.0-Paramecium_tetraurelia-noref/ -F 0.05 -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_tetraurelia-noref/tmp/mergeSam_fileyNrdmV
cuffcompare -o tmp_meta_asm -C -G  cuffmerge-2.2.0-Paramecium_tetraurelia-noref//transcripts.gtf
cuffcompare -o tmp_meta_asm -C -G  cuffmerge-2.2.0-Paramecium_tetraurelia-noref//merged.gtf