ls */accepted_hits/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 -g /data/results/reference/mmu/mm10/Mus_musculus.GRCm38.84.last500nt.gtf2  assemblies.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 F16,F16mut --no-length-correction --library-type fr-secondstrand --no-update-check --num-threads 10 -q -o cuffdiff_F16_vs_F16mut  merged_asm/merged.gtf SC3R6-1F16.bam2,SC3R7-6F16.bam2 SC3R8-2F16mut.bam2,SC3R9-5F16mut.bam2,SC3R10-8F16mut.bam2 &> cuffdiff_F16_vs_F16mut.log

cuffdiff -L M14,M14mut --no-length-correction --library-type fr-secondstrand --no-update-check --num-threads 10 -q -o cuffdiff_M14_vs_M14mut  merged_asm/merged.gtf SC3R1-1M14.bam2,SC3R2-3M14.bam2 SC3R3-6M14mut.bam2,SC3R4-8M14mut.bam2,SC3R5-9M14mut.bam2 &> cuffdiff_M14_vs_M14mut.log