/data/results/tools/align/cufflinks-2.2.1.Linux_x86_64/cuffmerge -p 8 -s /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome.fa -o merged_asm2 -g /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf assemblies.txt2
gtf_to_sam -F SCR10-E145-4wt/accepted_hits_ensembl_novel/transcripts.gtf merged_asm2/tmp/gtf2sam_fileYURypb
gtf_to_sam -F SCR12-E145-6Het/accepted_hits_ensembl_novel/transcripts.gtf merged_asm2/tmp/gtf2sam_filex9Neqw
gtf_to_sam -F SCR13-E145-3wt/accepted_hits_ensembl_novel/transcripts.gtf merged_asm2/tmp/gtf2sam_filemiir2f
gtf_to_sam -F SCR15-E145Het7/accepted_hits_ensembl_novel/transcripts.gtf merged_asm2/tmp/gtf2sam_fileo9mBhu
sort -k 3,3 -k 4,4n --temporary-directory=merged_asm2/tmp/ merged_asm2/tmp/gtf2sam_fileYURypb merged_asm2/tmp/gtf2sam_filex9Neqw merged_asm2/tmp/gtf2sam_filemiir2f merged_asm2/tmp/gtf2sam_fileo9mBhu > merged_asm2/tmp/mergeSam_fileK2u3D6
cufflinks -o merged_asm2/ -F 0.05 -g /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 8 merged_asm2/tmp/mergeSam_fileK2u3D6
cuffcompare -o tmp_meta_asm -C -G  -r /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf  -s /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome.fa merged_asm2//transcripts.gtf
cuffcompare -o tmp_meta_asm -C -G  -r /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf  -s /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome.fa merged_asm2//merged.gtf