#template
#/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie .bam -p 8 -o .gtf -A .tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> .log

/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_0h_replicate_Ib/accepted_hits.bam -p 10 -o  ballgown/KO_0h_replicate_I/KO_0h_replicate_I.gtf -A ballgown/KO_0h_replicate_I/KO_0h_replicate_I.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> KO_0h_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_0h_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/KO_0h_replicate_II/KO_0h_replicate_II.gtf -A ballgown/KO_0h_replicate_II/KO_0h_replicate_II.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> KO_0h_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_2h_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/KO_2h_replicate_I/KO_2h_replicate_I.gtf -A ballgown/KO_2h_replicate_I/KO_2h_replicate_I.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> KO_2h_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_2h_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/KO_2h_replicate_II/KO_2h_replicate_II.gtf -A ballgown/KO_2h_replicate_II/KO_2h_replicate_II.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> KO_2h_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_6h_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/KO_6h_replicate_I/KO_6h_replicate_I.gtf -A ballgown/KO_6h_replicate_I/KO_6h_replicate_I.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> KO_6h_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_6h_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/KO_6h_replicate_II/KO_6h_replicate_II.gtf -A ballgown/KO_6h_replicate_II/KO_6h_replicate_II.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> KO_6h_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_IFN-gamma_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/KO_IFN-gamma_replicate_II/KO_IFN-gamma_replicate_II.gtf -A ballgown/KO_IFN-gamma_replicate_II/KO_IFN-gamma_replicate_II.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> KO_IFN-gamma_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_IFN_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/KO_IFN_replicate_I/KO_IFN_replicate_I.gtf -A ballgown/KO_IFN_replicate_I/KO_IFN_replicate_I.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> KO_IFN_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_0h_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/WT_0h_replicate_I/WT_0h_replicate_I.gtf -A ballgown/WT_0h_replicate_I/WT_0h_replicate_I.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> WT_0h_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_0h_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/WT_0h_replicate_II/WT_0h_replicate_II.gtf -A ballgown/WT_0h_replicate_II/WT_0h_replicate_II.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> WT_0h_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_2h_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/WT_2h_replicate_I/WT_2h_replicate_I.gtf -A ballgown/WT_2h_replicate_I/WT_2h_replicate_I.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> WT_2h_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_2h_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/WT_2h_replicate_II/WT_2h_replicate_II.gtf -A ballgown/WT_2h_replicate_II/WT_2h_replicate_II.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> WT_2h_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_6h_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/WT_6h_replicate_I/WT_6h_replicate_I.gtf -A ballgown/WT_6h_replicate_I/WT_6h_replicate_I.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> WT_6h_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_6h_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/WT_6h_replicate_II/WT_6h_replicate_II.gtf -A ballgown/WT_6h_replicate_II/WT_6h_replicate_II.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> WT_6h_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_IFN-gamma_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/WT_IFN-gamma_replicate_I/WT_IFN-gamma_replicate_I.gtf -A ballgown/WT_IFN-gamma_replicate_I/WT_IFN-gamma_replicate_I.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> WT_IFN-gamma_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_IFN-gamma_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/WT_IFN-gamma_replicate_II/WT_IFN-gamma_replicate_II.gtf -A ballgown/WT_IFN-gamma_replicate_II/WT_IFN-gamma_replicate_II.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> WT_IFN-gamma_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_IL4_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/WT_IL4_replicate_I/WT_IL4_replicate_I.gtf -A ballgown/WT_IL4_replicate_I/WT_IL4_replicate_I.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> WT_IL4_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_IL4_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/WT_IL4_replicate_II/WT_IL4_replicate_II.gtf -A ballgown/WT_IL4_replicate_II/WT_IL4_replicate_II.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> WT_IL4_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_IL4_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/KO_IL4_replicate_I/KO_IL4_replicate_I.gtf -A ballgown/KO_IL4_replicate_I/KO_IL4_replicate_I.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> KO_IL4_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_IL4_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/KO_IL4_replicate_II/KO_IL4_replicate_II.gtf -A ballgown/KO_IL4_replicate_II/KO_IL4_replicate_II.tab -B -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf &> KO_IL4_replicate_II.log

/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 ballgown/KO_0h_replicate_II/KO_0h_replicate_II.gtf ballgown/KO_0h_replicate_I/KO_0h_replicate_I.gtf ballgown/KO_2h_replicate_II/KO_2h_replicate_II.gtf ballgown/KO_2h_replicate_I/KO_2h_replicate_I.gtf ballgown/KO_6h_replicate_II/KO_6h_replicate_II.gtf ballgown/KO_6h_replicate_I/KO_6h_replicate_I.gtf ballgown/KO_IFN-gamma_replicate_II/KO_IFN-gamma_replicate_II.gtf ballgown/KO_IFN_replicate_I/KO_IFN_replicate_I.gtf ballgown/KO_IL4_replicate_II/KO_IL4_replicate_II.gtf ballgown/KO_IL4_replicate_I/KO_IL4_replicate_I.gtf ballgown/WT_0h_replicate_II/WT_0h_replicate_II.gtf ballgown/WT_0h_replicate_I/WT_0h_replicate_I.gtf ballgown/WT_2h_replicate_II/WT_2h_replicate_II.gtf ballgown/WT_2h_replicate_I/WT_2h_replicate_I.gtf ballgown/WT_6h_replicate_II/WT_6h_replicate_II.gtf ballgown/WT_6h_replicate_I/WT_6h_replicate_I.gtf ballgown/WT_IFN-gamma_replicate_II/WT_IFN-gamma_replicate_II.gtf ballgown/WT_IFN-gamma_replicate_I/WT_IFN-gamma_replicate_I.gtf ballgown/WT_IL4_replicate_II/WT_IL4_replicate_II.gtf ballgown/WT_IL4_replicate_I/WT_IL4_replicate_I.gtf


/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_0h_replicate_Ib/accepted_hits.bam -p 10 -o  ballgown/KO_0h_replicate_I/KO_0h_replicate_I.gtf -e -B  -G merged.gtf &> KO_0h_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_0h_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/KO_0h_replicate_II/KO_0h_replicate_II.gtf -e -B  -G merged.gtf &> KO_0h_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_2h_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/KO_2h_replicate_I/KO_2h_replicate_I.gtf -e -B  -G merged.gtf &> KO_2h_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_2h_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/KO_2h_replicate_II/KO_2h_replicate_II.gtf -e -B  -G merged.gtf &> KO_2h_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_6h_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/KO_6h_replicate_I/KO_6h_replicate_I.gtf -e -B  -G merged.gtf &> KO_6h_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_6h_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/KO_6h_replicate_II/KO_6h_replicate_II.gtf -e -B  -G merged.gtf &> KO_6h_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_IFN-gamma_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/KO_IFN-gamma_replicate_II/KO_IFN-gamma_replicate_II.gtf -e -B  -G merged.gtf &> KO_IFN-gamma_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_IFN_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/KO_IFN_replicate_I/KO_IFN_replicate_I.gtf -e -B  -G merged.gtf &> KO_IFN_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_IL4_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/KO_IL4_replicate_I/KO_IL4_replicate_I.gtf -e -B  -G merged.gtf &> KO_IL4_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/KO_IL4_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/KO_IL4_replicate_II/KO_IL4_replicate_II.gtf -e -B  -G merged.gtf &> KO_IL4_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_0h_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/WT_0h_replicate_I/WT_0h_replicate_I.gtf -e -B  -G merged.gtf &> WT_0h_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_0h_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/WT_0h_replicate_II/WT_0h_replicate_II.gtf -e -B  -G merged.gtf &> WT_0h_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_2h_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/WT_2h_replicate_I/WT_2h_replicate_I.gtf -e -B  -G merged.gtf &> WT_2h_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_2h_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/WT_2h_replicate_II/WT_2h_replicate_II.gtf -e -B  -G merged.gtf &> WT_2h_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_6h_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/WT_6h_replicate_I/WT_6h_replicate_I.gtf -e -B  -G merged.gtf &> WT_6h_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_6h_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/WT_6h_replicate_II/WT_6h_replicate_II.gtf -e -B  -G merged.gtf &> WT_6h_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_IFN-gamma_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/WT_IFN-gamma_replicate_I/WT_IFN-gamma_replicate_I.gtf -e -B  -G merged.gtf &> WT_IFN-gamma_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_IFN-gamma_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/WT_IFN-gamma_replicate_II/WT_IFN-gamma_replicate_II.gtf -e -B  -G merged.gtf &> WT_IFN-gamma_replicate_II.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_IL4_replicate_Ib/accepted_hits.bam -p 10 -o ballgown/WT_IL4_replicate_I/WT_IL4_replicate_I.gtf -e -B  -G merged.gtf &> WT_IL4_replicate_I.log
/data/results/tools/rnaseq/stringtie/stringtie-1.3.3b.Linux_x86_64/stringtie ../tophat/WT_IL4_replicate_IIb/accepted_hits.bam -p 10 -o ballgown/WT_IL4_replicate_II/WT_IL4_replicate_II.gtf -e -B  -G merged.gtf &> WT_IL4_replicate_II.log

/data/results/tools/rnaseq/stringtie/stringtie-master/prepDE.py

/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/edgeR1.r
#ls edgeRtranscripts-?h.csv > edgeR-results.txt
#ls edgeRtranscripts-???.csv >> edgeR-results.txt
#awk -v f="/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/merged.gtf" -f addGeneToEdger.awk
#cat edgeR-results.txt | awk -v f="/data/images/proton/DKlab/mr/Polysomes/reads/stringtie/merged.gtf" -f addGeneToEdger.awk