/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-C2-1_Diff_rep1-GSM3028917.GENCODEV25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa C2-1_Diff_rep1-GSM3028917.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-C2-1_Undiff_rep1-GSM3028913.GENCODEV25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa C2-1_Undiff_rep1-GSM3028913.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-C2-2_Diff_rep1-GSM3028918.GENCODEV25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa C2-2_Diff_rep1-GSM3028918.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-C2-2_Undiff_rep1-GSM3028914.GENCODEV25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa C2-2_Undiff_rep1-GSM3028914.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-R2-1_Diff_rep1-GSM3028919.GENCODEV25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa R2-1_Diff_rep1-GSM3028919.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-R2-1_Undiff_rep1-GSM3028915.GENCODEV25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa R2-1_Undiff_rep1-GSM3028915.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-R2-2_Diff_rep1-GSM3028920.GENCODEV25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa R2-2_Diff_rep1-GSM3028920.a.e200.offrate1.bam
/oak/stanford/groups/akundaje/marinovg/programs/express-1.5.1-linux_x86_64/express --rf-stranded -o express-1.5.1-R2-2_Undiff_rep1-GSM3028916.GENCODEV25 /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.fa R2-2_Undiff_rep1-GSM3028916.a.e200.offrate1.bam