ls */accepted_hits3/transcripts.gtf > assemblies.txt
PATH=/data/results/tools/align/cufflinks-2.2.1.Linux_x86_64:$PATH; export PATH

/data/results/tools/align/cufflinks-2.2.1.Linux_x86_64/cuffmerge   -p 8 -s /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa -o merged_asm-with-rerun-G1-U2 -g /data/results/reference/mmu/mm10/Mus_musculus.GRCm38.84.last500nt.gtf2  assemblies-with-rerun-G1-U2.txt


#/data/results/tools/align/cufflinks-2.2.1.Linux_x86_64/cuffmerge   -p 8 -s /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa -o merged_asm -g /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Archives/archive-2013-03-06-15-01-24/Genes/genes.gtf  assemblies.txt
#reczko@max:/data/images/proton/run44/mm10/tophat_005$ samtools reheader /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.dict sort_uniq.bam > sort_uniq.bam2
#reczko@max:/data/images/proton/run44/mm10/tophat_005$ cd ../tophat_006
#reczko@max:/data/images/proton/run44/mm10/tophat_006$ samtools reheader /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.dict sort_uniq.bam > sort_uniq.bam2
#/data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf


cuffdiff -L Gcondition,U --no-length-correction --library-type fr-secondstrand --no-update-check --num-threads 10 -q -o cuffdiff_G_vs_U-with-rerun-G1-U2  merged_asm-with-rerun-G1-U2/merged.gtf GK3R7-G1.bam2,GK3R8-G2.bam2,GK3R9-G3.bam2,GK3R7r-G1.bam2 GK3R4-U1.bam2,GK3R5-U2.bam2,GK3R6-U3.bam2,GK3R5r-U2.bam2 &> cuffdiff_G_vs_U-with-rerun-G1-U2.log