cd /data/images/proton/DKlab/orsalia/stringtie/ /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt01pos.sorted.bam -p 8 -e -o PCG_wt01.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt02pos.sorted.bam -p 8 -e -o PCG_wt02.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt21pos.bam -p 8 -e -o PCG_wt21.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt22pos.bam -p 8 -e -o PCG_wt22.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt61pos.bam -p 8 -e -o PCG_wt61.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt62pos.bam -p 8 -e -o PCG_wt62.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwtIFN1pos.bam -p 8 -e -o PCG_wtIFN1.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwtIFN2pos.bam -p 8 -e -o PCG_wtIFN2.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt01IL4pos.bam -p 8 -e -o PCG_wt01IL4.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt02IL4pos.bam -p 8 -e -o PCG_wt02IL4.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo01pos.sorted.bam -p 8 -e -o PCG_Ko01.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo02pos.sorted.bam -p 8 -e -o PCG_Ko02.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKO21pos.bam -p 8 -e -o PCG_KO21.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKO22pos.bam -p 8 -e -o PCG_KO22.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo61pos.bam -p 8 -e -o PCG_Ko61.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo62pos.bam -p 8 -e -o PCG_Ko62.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKOIFN1pos.bam -p 8 -e -o PCG_KOIFN1.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKOIFN2pos.bam -p 8 -e -o PCG_KOIFN2.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo1IL4pos.bam -p 8 -e -o PCG_Ko1IL4.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo2IL4pos.bam -p 8 -e -o PCG_Ko2IL4.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf cd ~/bak/doc/fleming/kafasla/DKlab/mr/Polysomes/www/ echo KO_0h_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_0h_replicate_I.bam -p 8 -e -o PCG_KO_0h_replicate_I.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo KO_0h_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_0h_replicate_II.bam -p 8 -e -o PCG_KO_0h_replicate_II.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo KO_2h_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_2h_replicate_I.bam -p 8 -e -o PCG_KO_2h_replicate_I.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo KO_2h_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_2h_replicate_II.bam -p 8 -e -o PCG_KO_2h_replicate_II.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo KO_6h_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_6h_replicate_I.bam -p 8 -e -o PCG_KO_6h_replicate_I.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo KO_6h_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_6h_replicate_II.bam -p 8 -e -o PCG_KO_6h_replicate_II.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo KO_IFN-gamma_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_IFN-gamma_replicate_I.bam -p 8 -e -o PCG_KO_IFN-gamma_replicate_I.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo KO_IFN-gamma_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_IFN-gamma_replicate_II.bam -p 8 -e -o PCG_KO_IFN-gamma_replicate_II.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo KO_IL4_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_IL4_replicate_I.bam -p 8 -e -o PCG_KO_IL4_replicate_I.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo KO_IL4_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_IL4_replicate_II.bam -p 8 -e -o PCG_KO_IL4_replicate_II.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo WT_0h_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_0h_replicate_I.bam -p 8 -e -o PCG_WT_0h_replicate_I.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo WT_0h_replicate_II_.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_0h_replicate_II_.bam -p 8 -e -o PCG_WT_0h_replicate_II_.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo WT_2h_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_2h_replicate_I.bam -p 8 -e -o PCG_WT_2h_replicate_I.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo WT_2h_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_2h_replicate_II.bam -p 8 -e -o PCG_WT_2h_replicate_II.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo WT_6h_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_6h_replicate_I.bam -p 8 -e -o PCG_WT_6h_replicate_I.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo WT_6h_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_6h_replicate_II.bam -p 8 -e -o PCG_WT_6h_replicate_II.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo WT_IFN-gamma_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_IFN-gamma_replicate_I.bam -p 8 -e -o PCG_WT_IFN-gamma_replicate_I.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo WT_IFN-gamma_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_IFN-gamma_replicate_II.bam -p 8 -e -o PCG_WT_IFN-gamma_replicate_II.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo WT_IL4_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_IL4_replicate_I.bam -p 8 -e -o PCG_WT_IL4_replicate_I.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf echo WT_IL4_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_IL4_replicate_II.bam -p 8 -e -o PCG_WT_IL4_replicate_II.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -o PCG_merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_Ko01.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_Ko1IL4.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_KO22.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_Ko61.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_KOIFN1.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_wt01.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_wt02.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_wt21.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_wt61.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_wtIFN1.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_Ko02.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_KO21.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_Ko2IL4.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_Ko62.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_KOIFN2.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_wt01IL4.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_wt02IL4.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_wt22.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_wt62.gtf /data/images/proton/DKlab/orsalia/stringtie/PCG_wtIFN2.gtf PCG_KO_0h_replicate_I.gtf PCG_KO_0h_replicate_II.gtf PCG_KO_2h_replicate_I.gtf PCG_KO_2h_replicate_II.gtf PCG_KO_6h_replicate_I.gtf PCG_KO_6h_replicate_II.gtf PCG_KO_IFN-gamma_replicate_I.gtf PCG_KO_IFN-gamma_replicate_II.gtf PCG_KO_IL4_replicate_I.gtf PCG_KO_IL4_replicate_II.gtf PCG_WT_0h_replicate_I.gtf PCG_WT_0h_replicate_II_.gtf PCG_WT_2h_replicate_I.gtf PCG_WT_2h_replicate_II.gtf PCG_WT_6h_replicate_I.gtf PCG_WT_6h_replicate_II.gtf PCG_WT_IFN-gamma_replicate_I.gtf PCG_WT_IFN-gamma_replicate_II.gtf PCG_WT_IL4_replicate_I.gtf PCG_WT_IL4_replicate_II.gtf #/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -o PCG_merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf PCG_KO_0h_replicate_I.gtf PCG_KO_0h_replicate_II.gtf PCG_KO_2h_replicate_I.gtf PCG_KO_2h_replicate_II.gtf PCG_KO_6h_replicate_I.gtf PCG_KO_6h_replicate_II.gtf PCG_KO_IFN-gamma_replicate_I.gtf PCG_KO_IFN-gamma_replicate_II.gtf PCG_KO_IL4_replicate_I.gtf PCG_KO_IL4_replicate_II.gtf PCG_WT_0h_replicate_I.gtf PCG_WT_0h_replicate_II_.gtf PCG_WT_2h_replicate_I.gtf PCG_WT_2h_replicate_II.gtf PCG_WT_6h_replicate_I.gtf PCG_WT_6h_replicate_II.gtf PCG_WT_IFN-gamma_replicate_I.gtf PCG_WT_IFN-gamma_replicate_II.gtf PCG_WT_IL4_replicate_I.gtf PCG_WT_IL4_replicate_II.gtf #/data/results/tools/rnaseq/stringtie/gffcompare-0.10.1.Linux_x86_64/gffcompare -r /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.pcg.gtf -o PCG_compare1 merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt01pos.sorted.bam -p 8 -e -B -o PCG_ballgown/wt01/wt01.merged.gtf -G PCG_merged.gtf & /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt02pos.sorted.bam -p 8 -e -B -o PCG_ballgown/wt02/wt02.merged.gtf -G PCG_merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt21pos.bam -p 8 -e -B -o PCG_ballgown/wt21/wt21.merged.gtf -G PCG_merged.gtf & /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt22pos.bam -p 8 -e -B -o PCG_ballgown/wt22/wt22.merged.gtf -G PCG_merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt61pos.bam -p 8 -e -B -o PCG_ballgown/wt61/wt61.merged.gtf -G PCG_merged.gtf & /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt62pos.bam -p 8 -e -B -o PCG_ballgown/wt62/wt62.merged.gtf -G PCG_merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwtIFN1pos.bam -p 8 -e -B -o PCG_ballgown/wtIFN1/wtIFN1.merged.gtf -G PCG_merged.gtf & /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwtIFN2pos.bam -p 8 -e -B -o PCG_ballgown/wtIFN2/wtIFN2.merged.gtf -G PCG_merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt01IL4pos.bam -p 8 -e -B -o PCG_ballgown/wt01IL4/wt01IL4.merged.gtf -G PCG_merged.gtf & /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedwt02IL4pos.bam -p 8 -e -B -o PCG_ballgown/wt02IL4/wt02IL4.merged.gtf -G PCG_merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo01pos.sorted.bam -p 8 -e -B -o PCG_ballgown/Ko01/Ko01.merged.gtf -G PCG_merged.gtf & /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo02pos.sorted.bam -p 8 -e -B -o PCG_ballgown/Ko02/Ko02.merged.gtf -G PCG_merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKO21pos.bam -p 8 -e -B -o PCG_ballgown/KO21/KO21.merged.gtf -G PCG_merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKO22pos.bam -p 8 -e -B -o PCG_ballgown/KO22/KO22.merged.gtf -G PCG_merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo61pos.bam -p 8 -e -B -o PCG_ballgown/Ko61/Ko61.merged.gtf -G PCG_merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo62pos.bam -p 8 -e -B -o PCG_ballgown/Ko62/Ko62.merged.gtf -G PCG_merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKOIFN1pos.bam -p 8 -e -B -o PCG_ballgown/KOIFN1/KOIFN1.merged.gtf -G PCG_merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKOIFN2pos.bam -p 8 -e -B -o PCG_ballgown/KOIFN2/KOIFN2.merged.gtf -G PCG_merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo1IL4pos.bam -p 8 -e -B -o PCG_ballgown/Ko1IL4/Ko1IL4.merged.gtf -G PCG_merged.gtf /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie /data/images/proton/DKlab/orsalia/sortedKo2IL4pos.bam -p 8 -e -B -o PCG_ballgown/Ko2IL4/Ko2IL4.merged.gtf -G PCG_merged.gtf echo KO_0h_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_0h_replicate_I.bam -p 8 -e -B -o PCG_ballgown/PCG_KO_0h_replicate_I/KO_0h_replicate_I.merged.gtf -G PCG_merged.gtf #mv KO_0h_replicate_I PCG_ballgown echo KO_0h_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_0h_replicate_II.bam -p 8 -e -B -o PCG_ballgown/PCG_KO_0h_replicate_II/KO_0h_replicate_II.merged.gtf -G PCG_merged.gtf #mv KO_0h_replicate_II PCG_ballgown echo KO_2h_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_2h_replicate_I.bam -p 8 -e -B -o PCG_ballgown/PCG_KO_2h_replicate_I/KO_2h_replicate_I.merged.gtf -G PCG_merged.gtf #mv KO_2h_replicate_I PCG_ballgown echo KO_2h_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_2h_replicate_II.bam -p 8 -e -B -o PCG_ballgown/PCG_KO_2h_replicate_II/KO_2h_replicate_II.merged.gtf -G PCG_merged.gtf #mv KO_2h_replicate_II PCG_ballgown echo KO_6h_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_6h_replicate_I.bam -p 8 -e -B -o PCG_ballgown/PCG_KO_6h_replicate_I/KO_6h_replicate_I.merged.gtf -G PCG_merged.gtf #mv KO_6h_replicate_I PCG_ballgown echo KO_6h_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_6h_replicate_II.bam -p 8 -e -B -o PCG_ballgown/PCG_KO_6h_replicate_II/KO_6h_replicate_II.merged.gtf -G PCG_merged.gtf #mv KO_6h_replicate_II PCG_ballgown echo KO_IFN-gamma_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_IFN-gamma_replicate_I.bam -p 8 -e -B -o PCG_ballgown/PCG_KO_IFN-gamma_replicate_I/KO_IFN-gamma_replicate_I.merged.gtf -G PCG_merged.gtf #mv KO_IFN-gamma_replicate_I PCG_ballgown echo KO_IFN-gamma_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_IFN-gamma_replicate_II.bam -p 8 -e -B -o PCG_ballgown/PCG_KO_IFN-gamma_replicate_II/KO_IFN-gamma_replicate_II.merged.gtf -G PCG_merged.gtf #mv KO_IFN-gamma_replicate_II PCG_ballgown echo KO_IL4_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_IL4_replicate_I.bam -p 8 -e -B -o PCG_ballgown/PCG_KO_IL4_replicate_I/KO_IL4_replicate_I.merged.gtf -G PCG_merged.gtf #mv KO_IL4_replicate_I PCG_ballgown echo KO_IL4_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie KO_IL4_replicate_II.bam -p 8 -e -B -o PCG_ballgown/PCG_KO_IL4_replicate_II/KO_IL4_replicate_II.merged.gtf -G PCG_merged.gtf #mv KO_IL4_replicate_II PCG_ballgown echo WT_0h_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_0h_replicate_I.bam -p 8 -e -B -o PCG_ballgown/PCG_WT_0h_replicate_I/WT_0h_replicate_I.merged.gtf -G PCG_merged.gtf #mv WT_0h_replicate_I PCG_ballgown echo WT_0h_replicate_II_.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_0h_replicate_II_.bam -p 8 -e -B -o PCG_ballgown/PCG_WT_0h_replicate_II_/WT_0h_replicate_II_.merged.gtf -G PCG_merged.gtf #mv WT_0h_replicate_II_ PCG_ballgown echo WT_2h_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_2h_replicate_I.bam -p 8 -e -B -o PCG_ballgown/PCG_WT_2h_replicate_I/WT_2h_replicate_I.merged.gtf -G PCG_merged.gtf #mv WT_2h_replicate_I PCG_ballgown echo WT_2h_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_2h_replicate_II.bam -p 8 -e -B -o PCG_ballgown/PCG_WT_2h_replicate_II/WT_2h_replicate_II.merged.gtf -G PCG_merged.gtf #mv WT_2h_replicate_II PCG_ballgown echo WT_6h_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_6h_replicate_I.bam -p 8 -e -B -o PCG_ballgown/PCG_WT_6h_replicate_I/WT_6h_replicate_I.merged.gtf -G PCG_merged.gtf #mv WT_6h_replicate_I PCG_ballgown echo WT_6h_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_6h_replicate_II.bam -p 8 -e -B -o PCG_ballgown/PCG_WT_6h_replicate_II/WT_6h_replicate_II.merged.gtf -G PCG_merged.gtf #mv WT_6h_replicate_II PCG_ballgown echo WT_IFN-gamma_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_IFN-gamma_replicate_I.bam -p 8 -e -B -o PCG_ballgown/PCG_WT_IFN-gamma_replicate_I/WT_IFN-gamma_replicate_I.merged.gtf -G PCG_merged.gtf #mv WT_IFN-gamma_replicate_I PCG_ballgown echo WT_IFN-gamma_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_IFN-gamma_replicate_II.bam -p 8 -e -B -o PCG_ballgown/PCG_WT_IFN-gamma_replicate_II/WT_IFN-gamma_replicate_II.merged.gtf -G PCG_merged.gtf #mv WT_IFN-gamma_replicate_II PCG_ballgown echo WT_IL4_replicate_I.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_IL4_replicate_I.bam -p 8 -e -B -o PCG_ballgown/PCG_WT_IL4_replicate_I/WT_IL4_replicate_I.merged.gtf -G PCG_merged.gtf #mv WT_IL4_replicate_I PCG_ballgown echo WT_IL4_replicate_II.bam /data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie WT_IL4_replicate_II.bam -p 8 -e -B -o PCG_ballgown/PCG_WT_IL4_replicate_II/WT_IL4_replicate_II.merged.gtf -G PCG_merged.gtf #mv WT_IL4_replicate_II PCG_ballgown /data/results/tools/rnaseq/stringtie/stringtie-master/prepDE.py