/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression -p 8 --calc-ci --append-names --bowtie2 --bowtie2-path /oak/stanford/groups/akundaje/marinovg/programs/bowtie2-2.1.0 --strandedness forward --paired-end -p 8 /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d25.RAMPAGE.b1.half_of_reads.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d25.RAMPAGE.b1.half_of_reads.end2.fastq.gz /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/RSEM/stringtie1.3.3b.PolyA+Total-with_annotation.merge RSEM/primary_keratinocyte-d25.RAMPAGE.b1_half_of_reads/stringtie1.3.3b.PolyA+Total-with_annotation.merge