/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression -p 8 --calc-ci --append-names --star --star-gzipped-read-file --star-path /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/ --strandedness reverse --paired-end -p 8 /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d0.RNA-seq_polyA.b1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d0.RNA-seq_polyA.b1.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-d0.RNA-seq_polyA.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 --star --star-gzipped-read-file --star-path /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/ --strandedness reverse --paired-end -p 8 /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d0.RNA-seq_polyA.b2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d0.RNA-seq_polyA.b2.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-d0.RNA-seq_polyA.b2/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 --star --star-gzipped-read-file --star-path /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/ --strandedness reverse --paired-end -p 8 /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d3.RNA-seq_polyA.b1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d3.RNA-seq_polyA.b1.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-d3.RNA-seq_polyA.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 --star --star-gzipped-read-file --star-path /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/ --strandedness reverse --paired-end -p 8 /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d3.RNA-seq_polyA.b2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d3.RNA-seq_polyA.b2.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-d3.RNA-seq_polyA.b2/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 --star --star-gzipped-read-file --star-path /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/ --strandedness reverse --paired-end -p 8 /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d6.RNA-seq_polyA.b1.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d6.RNA-seq_polyA.b1.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-d6.RNA-seq_polyA.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 --star --star-gzipped-read-file --star-path /oak/stanford/groups/akundaje/marinovg/programs/STAR-2.5.3a/bin/Linux_x86_64_static/ --strandedness reverse --paired-end -p 8 /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d6.RNA-seq_polyA.b2.end1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d6.RNA-seq_polyA.b2.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-d6.RNA-seq_polyA.b2/stringtie1.3.3b.PolyA+Total-with_annotation.merge
