/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 20 --compatible-hits-norm --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --output-dir C2-1_Diff_rep1-GSM3028917-2x75mers-STAR-2.5.3a-GENCODE_V26/Cufflinks-2.0.2-GENCODE-V25 C2-1_Diff_rep1-GSM3028917-2x75mers-STAR-2.5.3a-GENCODE_V26/STAR-2.5.3aAligned.sortedByCoord.out.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 20 --compatible-hits-norm --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --output-dir C2-1_Undiff_rep1-GSM3028913-2x75mers-STAR-2.5.3a-GENCODE_V26/Cufflinks-2.0.2-GENCODE-V25 C2-1_Undiff_rep1-GSM3028913-2x75mers-STAR-2.5.3a-GENCODE_V26/STAR-2.5.3aAligned.sortedByCoord.out.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 20 --compatible-hits-norm --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --output-dir C2-2_Diff_rep1-GSM3028918-2x75mers-STAR-2.5.3a-GENCODE_V26/Cufflinks-2.0.2-GENCODE-V25 C2-2_Diff_rep1-GSM3028918-2x75mers-STAR-2.5.3a-GENCODE_V26/STAR-2.5.3aAligned.sortedByCoord.out.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 20 --compatible-hits-norm --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --output-dir C2-2_Undiff_rep1-GSM3028914-2x75mers-STAR-2.5.3a-GENCODE_V26/Cufflinks-2.0.2-GENCODE-V25 C2-2_Undiff_rep1-GSM3028914-2x75mers-STAR-2.5.3a-GENCODE_V26/STAR-2.5.3aAligned.sortedByCoord.out.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 20 --compatible-hits-norm --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --output-dir R2-1_Diff_rep1-GSM3028919-2x75mers-STAR-2.5.3a-GENCODE_V26/Cufflinks-2.0.2-GENCODE-V25 R2-1_Diff_rep1-GSM3028919-2x75mers-STAR-2.5.3a-GENCODE_V26/STAR-2.5.3aAligned.sortedByCoord.out.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 20 --compatible-hits-norm --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --output-dir R2-1_Undiff_rep1-GSM3028915-2x75mers-STAR-2.5.3a-GENCODE_V26/Cufflinks-2.0.2-GENCODE-V25 R2-1_Undiff_rep1-GSM3028915-2x75mers-STAR-2.5.3a-GENCODE_V26/STAR-2.5.3aAligned.sortedByCoord.out.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 20 --compatible-hits-norm --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --output-dir R2-2_Diff_rep1-GSM3028920-2x75mers-STAR-2.5.3a-GENCODE_V26/Cufflinks-2.0.2-GENCODE-V25 R2-2_Diff_rep1-GSM3028920-2x75mers-STAR-2.5.3a-GENCODE_V26/STAR-2.5.3aAligned.sortedByCoord.out.bam
/oak/stanford/groups/akundaje/marinovg/programs/cufflinks-2.0.2.Linux_x86_64/cufflinks -p 20 --compatible-hits-norm --GTF /oak/stanford/groups/akundaje/marinovg/genomes/hg20/gencode/gencode_v25/gencode.v25.annotation.gtf --output-dir R2-2_Undiff_rep1-GSM3028916-2x75mers-STAR-2.5.3a-GENCODE_V26/Cufflinks-2.0.2-GENCODE-V25 R2-2_Undiff_rep1-GSM3028916-2x75mers-STAR-2.5.3a-GENCODE_V26/STAR-2.5.3aAligned.sortedByCoord.out.bam