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

#wt_vs_ko
#wt_TCP_vs_ko_TCP
#wt_vs_wt_TCP
#ko_vs_ko_TCP

cuffdiff -L wt,ko --no-length-correction --library-type fr-secondstrand --no-update-check --num-threads 10 -q -o cuffdiff_wt_vs_ko  merged_asm/merged.gtf IT3R23-wt6.bam2,IT3R24-wt7.bam2,IT3R25-wt8.bam2,IT3R26-wt9.bam2 IT3R27-ko4.bam2,IT3R28-ko5.bam2,IT3R29-ko6.bam2,IT3R30-ko7.bam2 &> cuffdiff_wt_vs_ko.log

cuffdiff -L wtTCP,koTCP --no-length-correction --library-type fr-secondstrand --no-update-check --num-threads 10 -q -o cuffdiff_wtTCP_vs_koTCP  merged_asm/merged.gtf IT3R31-wt4TCP36.bam2,IT3R32-wt5TCP36.bam2 IT3R33-ko4TCP36.bam2,IT3R34-ko5TCP36.bam2 &> cuffdiff_wtTCP_vs_koTCP.log

cuffdiff -L wt,wtTCP --no-length-correction --library-type fr-secondstrand --no-update-check --num-threads 10 -q -o cuffdiff_wt_vs_wtTCP  merged_asm/merged.gtf IT3R23-wt6.bam2,IT3R24-wt7.bam2,IT3R25-wt8.bam2,IT3R26-wt9.bam2 IT3R31-wt4TCP36.bam2,IT3R32-wt5TCP36.bam2 &> cuffdiff_wt_vs_wtTCP.log

cuffdiff -L ko,koTCP --no-length-correction --library-type fr-secondstrand --no-update-check --num-threads 10 -q -o cuffdiff_ko_vs_koTCP  merged_asm/merged.gtf IT3R27-ko4.bam2,IT3R28-ko5.bam2,IT3R29-ko6.bam2,IT3R30-ko7.bam2 IT3R33-ko4TCP36.bam2,IT3R34-ko5TCP36.bam2 &> cuffdiff_ko_vs_koTCP.log