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 merged.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 -B -o KO_0h_replicate_II/KO_0h_replicate_II.merged.gtf -G merged.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 -B -o KO_2h_replicate_I/KO_2h_replicate_I.merged.gtf -G merged.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 -B -o KO_2h_replicate_II/KO_2h_replicate_II.merged.gtf -G merged.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 -B -o KO_6h_replicate_I/KO_6h_replicate_I.merged.gtf -G merged.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 -B -o KO_6h_replicate_II/KO_6h_replicate_II.merged.gtf -G merged.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 -B -o KO_IFN-gamma_replicate_I/KO_IFN-gamma_replicate_I.merged.gtf -G merged.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 -B -o KO_IFN-gamma_replicate_II/KO_IFN-gamma_replicate_II.merged.gtf -G merged.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 -B -o KO_IL4_replicate_I/KO_IL4_replicate_I.merged.gtf -G merged.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 -B -o KO_IL4_replicate_II/KO_IL4_replicate_II.merged.gtf -G merged.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 -B -o WT_0h_replicate_I/WT_0h_replicate_I.merged.gtf -G merged.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 -B -o WT_0h_replicate_II_/WT_0h_replicate_II_.merged.gtf -G merged.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 -B -o WT_2h_replicate_I/WT_2h_replicate_I.merged.gtf -G merged.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 -B -o WT_2h_replicate_II/WT_2h_replicate_II.merged.gtf -G merged.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 -B -o WT_6h_replicate_I/WT_6h_replicate_I.merged.gtf -G merged.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 -B -o WT_6h_replicate_II/WT_6h_replicate_II.merged.gtf -G merged.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 -B -o WT_IFN-gamma_replicate_I/WT_IFN-gamma_replicate_I.merged.gtf -G merged.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 -B -o WT_IFN-gamma_replicate_II/WT_IFN-gamma_replicate_II.merged.gtf -G merged.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 -B -o WT_IL4_replicate_I/WT_IL4_replicate_I.merged.gtf -G merged.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 -B -o WT_IL4_replicate_II/WT_IL4_replicate_II.merged.gtf -G merged.gtf