cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -p 8 stringtie1.3.3b.PolyA.files > stringtie1.3.3b.PolyA.merge.gtf
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -p 8 stringtie1.3.3b.Total.files > stringtie1.3.3b.Total.merge.gtf
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -p 8 stringtie1.3.3b.RAMPAGE.files > stringtie1.3.3b.RAMPAGE.merge.gtf
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -p 8 stringtie1.3.3b.PAS-seq.files > stringtie1.3.3b.PAS-seq.merge.gtf
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -p 8 stringtie1.3.3b.all_with_ribozero.files > stringtie1.3.3b.all_with_ribozero.merge.gtf
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -p 8 stringtie1.3.3b.all.files > stringtie1.3.3b.all.merge.gtf
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf stringtie1.3.3b.PolyA-with_annotation.files > stringtie1.3.3b.PolyA-with_annotation.merge.gtf
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf stringtie1.3.3b.Total-with_annotation.files > stringtie1.3.3b.Total-with_annotation.merge.gtf
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf stringtie1.3.3b.RAMPAGE-with_annotation.files > stringtie1.3.3b.RAMPAGE-with_annotation.merge.gtf
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf stringtie1.3.3b.PAS-seq-with_annotation.files > stringtie1.3.3b.PAS-seq-with_annotation.merge.gtf
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf stringtie1.3.3b.all_with_ribozero-with-annotation.files > stringtie1.3.3b.all_with_ribozero-with-annotation.merge.gtf
cd /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/2017-05-12-RNA-seq-remap; /oak/stanford/groups/akundaje/marinovg/programs/stringtie-1.3.3b.Linux_x86_64/stringtie --merge -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf stringtie1.3.3b.all-with-annotation.files > stringtie1.3.3b.all-with-annotation.merge.gtf