samtools view /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d0.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam | python /oak/stanford/groups/akundaje/marinovg/code/filterBAMsplices.py | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19.fa - -o /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d0.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.splices.bam
samtools view /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d0.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam | python /oak/stanford/groups/akundaje/marinovg/code/filterBAMsplices.py | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19.fa - -o /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d0.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.splices.bam
samtools view /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d3.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam | python /oak/stanford/groups/akundaje/marinovg/code/filterBAMsplices.py | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19.fa - -o /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d3.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.splices.bam
samtools view /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d3.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam | python /oak/stanford/groups/akundaje/marinovg/code/filterBAMsplices.py | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19.fa - -o /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d3.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.splices.bam
samtools view /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d6.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam | python /oak/stanford/groups/akundaje/marinovg/code/filterBAMsplices.py | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19.fa - -o /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d6.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.splices.bam
samtools view /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d6.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam | python /oak/stanford/groups/akundaje/marinovg/code/filterBAMsplices.py | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19.fa - -o /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/RNA-seq-polyA+/primary_keratinocyte-d6.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.splices.bam