/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -o merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf  /data/images/proton/DKlab/orsalia/stringtie/Ko01.gtf  /data/images/proton/DKlab/orsalia/stringtie/Ko1IL4.gtf  /data/images/proton/DKlab/orsalia/stringtie/KO22.gtf    /data/images/proton/DKlab/orsalia/stringtie/Ko61.gtf  /data/images/proton/DKlab/orsalia/stringtie/KOIFN1.gtf  /data/images/proton/DKlab/orsalia/stringtie/wt01.gtf     /data/images/proton/DKlab/orsalia/stringtie/wt02.gtf     /data/images/proton/DKlab/orsalia/stringtie/wt21.gtf  /data/images/proton/DKlab/orsalia/stringtie/wt61.gtf  /data/images/proton/DKlab/orsalia/stringtie/wtIFN1.gtf /data/images/proton/DKlab/orsalia/stringtie/Ko02.gtf  /data/images/proton/DKlab/orsalia/stringtie/KO21.gtf    /data/images/proton/DKlab/orsalia/stringtie/Ko2IL4.gtf  /data/images/proton/DKlab/orsalia/stringtie/Ko62.gtf  /data/images/proton/DKlab/orsalia/stringtie/KOIFN2.gtf  /data/images/proton/DKlab/orsalia/stringtie/wt01IL4.gtf  /data/images/proton/DKlab/orsalia/stringtie/wt02IL4.gtf  /data/images/proton/DKlab/orsalia/stringtie/wt22.gtf  /data/images/proton/DKlab/orsalia/stringtie/wt62.gtf  /data/images/proton/DKlab/orsalia/stringtie/wtIFN2.gtf KO_0h_replicate_I.gtf KO_0h_replicate_II.gtf KO_2h_replicate_I.gtf KO_2h_replicate_II.gtf KO_6h_replicate_I.gtf KO_6h_replicate_II.gtf KO_IFN-gamma_replicate_I.gtf KO_IFN-gamma_replicate_II.gtf KO_IL4_replicate_I.gtf KO_IL4_replicate_II.gtf WT_0h_replicate_I.gtf WT_0h_replicate_II_.gtf WT_2h_replicate_I.gtf WT_2h_replicate_II.gtf WT_6h_replicate_I.gtf WT_6h_replicate_II.gtf WT_IFN-gamma_replicate_I.gtf WT_IFN-gamma_replicate_II.gtf WT_IL4_replicate_I.gtf 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.gtf -o compare1 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 KO_0h_replicate_I/KO_0h_replicate_I.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv KO_0h_replicate_I 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 KO_0h_replicate_II/KO_0h_replicate_II.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv KO_0h_replicate_II 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 KO_2h_replicate_I/KO_2h_replicate_I.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv KO_2h_replicate_I 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 KO_2h_replicate_II/KO_2h_replicate_II.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv KO_2h_replicate_II 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 KO_6h_replicate_I/KO_6h_replicate_I.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv KO_6h_replicate_I 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 KO_6h_replicate_II/KO_6h_replicate_II.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv KO_6h_replicate_II 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 KO_IFN-gamma_replicate_I/KO_IFN-gamma_replicate_I.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv KO_IFN-gamma_replicate_I 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 KO_IFN-gamma_replicate_II/KO_IFN-gamma_replicate_II.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv KO_IFN-gamma_replicate_II 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 KO_IL4_replicate_I/KO_IL4_replicate_I.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv KO_IL4_replicate_I 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 KO_IL4_replicate_II/KO_IL4_replicate_II.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv KO_IL4_replicate_II 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 WT_0h_replicate_I/WT_0h_replicate_I.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv WT_0h_replicate_I 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 WT_0h_replicate_II_/WT_0h_replicate_II_.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv WT_0h_replicate_II_ 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 WT_2h_replicate_I/WT_2h_replicate_I.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv WT_2h_replicate_I 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 WT_2h_replicate_II/WT_2h_replicate_II.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv WT_2h_replicate_II 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 WT_6h_replicate_I/WT_6h_replicate_I.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv WT_6h_replicate_I 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 WT_6h_replicate_II/WT_6h_replicate_II.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv WT_6h_replicate_II 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 WT_IFN-gamma_replicate_I/WT_IFN-gamma_replicate_I.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv WT_IFN-gamma_replicate_I 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 WT_IFN-gamma_replicate_II/WT_IFN-gamma_replicate_II.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv WT_IFN-gamma_replicate_II 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 WT_IL4_replicate_I/WT_IL4_replicate_I.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv WT_IL4_replicate_I 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 WT_IL4_replicate_II/WT_IL4_replicate_II.merged.gtf -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf
mv WT_IL4_replicate_II ballgown
/data/results/tools/rnaseq/stringtie/stringtie-master/prepDE.py