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/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression -p 8 --calc-ci --append-names --bowtie-path /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch --strandedness reverse --paired-end -p 8 /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d60.GGR.Stanford_Khavari.PAS-seq.b1.t1.TGGATT.1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d60.GGR.Stanford_Khavari.PAS-seq.b1.t1.TGGATT.2.fastq.gz /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/RSEM/stringtie1.3.3b.PolyA+Total-with_annotation.merge RSEM/primary_keratinocyte-d60.PAS-seq.b1/stringtie1.3.3b.PolyA+Total-with_annotation.merge
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression -p 8 --calc-ci --append-names --bowtie-path /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch --strandedness reverse --paired-end -p 8 /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d60.GGR.Stanford_Khavari.PAS-seq.b2.t1.GATCAC.1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d60.GGR.Stanford_Khavari.PAS-seq.b2.t1.GATCAC.2.fastq.gz /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/annotations/RSEM/stringtie1.3.3b.PolyA+Total-with_annotation.merge RSEM/primary_keratinocyte-d60.PAS-seq.b2/stringtie1.3.3b.PolyA+Total-with_annotation.merge
