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 10 -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

#GBM_vs_LM
#GBF_vs_LF
#GBM_vs_GBF

#cuffdiff -L GBM,LM --no-length-correction --library-type fr-secondstrand --no-update-check --num-threads 10 -q -o cuffdiff_GBM_vs_LM  merged_asm/merged.gtf IT3R17-1GBM.bam2,IT3R18-9GBM.bam2,IT3R21-5GBaM.bam2 IT3R1-wt1LM.bam2,IT3R2-wt2LM.bam2,IT3R3-wt3LM.bam2,IT3R4-wt4LM.bam2   &> cuffdiff_GBM_vs_LM.log

cuffdiff -L GBF,LF --no-length-correction --library-type fr-secondstrand --no-update-check --num-threads 10 -q -o cuffdiff_GBF_vs_LF  merged_asm/merged.gtf IT3R19-8GBF.bam2,IT3R20-12GBF.bam2,IT3R22-3GMaF.bam2 IT3R5-wt1LF.bam2,IT3R6-wt2LF.bam2,IT3R7-wt3LF.bam2,IT3R8-wt4LF.bam2  &> cuffdiff_GBF_vs_LF.log
#mv cuffdiff_GBF_vs_LM.log cuffdiff_GBF_vs_LF.log

#cuffdiff -L GBM,GBF --no-length-correction --library-type fr-secondstrand --no-update-check --num-threads 10 -q -o cuffdiff_GBM_vs_GBF  merged_asm/merged.gtf IT3R17-1GBM.bam2,IT3R18-9GBM.bam2,IT3R21-5GBaM.bam2 IT3R19-8GBF.bam2,IT3R20-12GBF.bam2,IT3R22-3GMaF.bam2  &> cuffdiff_GBM_vs_GBF.log

#cuffdiff -L LM,LF --no-length-correction --library-type fr-secondstrand --no-update-check --num-threads 10 -q -o cuffdiff_LM_vs_LF  merged_asm/merged.gtf  IT3R1-wt1LM.bam2,IT3R2-wt2LM.bam2,IT3R3-wt3LM.bam2,IT3R4-wt4LM.bam2  IT3R5-wt1LF.bam2,IT3R6-wt2LF.bam2,IT3R7-wt3LF.bam2,IT3R8-wt4LF.bam2  &> cuffdiff_LM_vs_LM.log