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.b1.RAMPAGE/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.b1.RAMPAGE.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.b2.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam -p 8 > primary_keratinocyte-d30.b2.RAMPAGE.STAR-2.5.3a.stringtie1.3.3b.gtf