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 primary_keratinocyte-d20.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d20.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d20.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d20.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d25.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d25.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d25.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d25.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d30.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d30.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d30.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d30.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d35.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d35.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d35.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d35.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d40.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d40.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d40.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d40.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d45.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d45.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d45.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d45.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d50.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d50.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d50.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d50.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d55.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d55.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d55.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d55.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d60.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d60.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d60.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d60.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d00.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d00.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d00.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d00.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d05.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d05.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d05.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d05.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d10.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d10.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d10.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d10.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d15.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d15.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d15.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d15.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.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 primary_keratinocyte-d20.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d20.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d20.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d20.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d25.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d25.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d25.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d25.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d30.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d30.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d30.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d30.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d35.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d35.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d35.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d35.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d40.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d40.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d40.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d40.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d45.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d45.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d45.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d45.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d50.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d50.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d50.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d50.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d55.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d55.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d55.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d55.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d60.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d60.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d60.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d60.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d00.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d00.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d00.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d00.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d05.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d05.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d05.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d05.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d10.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d10.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d10.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d10.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d15.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d15.PAS-seq.b1.STAR-2.5.3a.stringtie1.3.3b.with-annotation.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 primary_keratinocyte-d15.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 -G /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf > primary_keratinocyte-d15.PAS-seq.b2.STAR-2.5.3a.stringtie1.3.3b.with-annotation.gtf