python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d00.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d00.PAS-seq.b1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d00.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d00.PAS-seq.b2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d05.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d05.PAS-seq.b1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d05.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d05.PAS-seq.b2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d10.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d10.PAS-seq.b1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d10.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d10.PAS-seq.b2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d15.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d15.PAS-seq.b1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d15.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d15.PAS-seq.b2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d20.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d20.PAS-seq.b1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d20.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d20.PAS-seq.b2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d25.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d25.PAS-seq.b1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d25.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d25.PAS-seq.b2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d30.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d30.PAS-seq.b1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d30.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d30.PAS-seq.b2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d35.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d35.PAS-seq.b1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d35.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d35.PAS-seq.b2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d40.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d40.PAS-seq.b1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d40.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d40.PAS-seq.b2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d45.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d45.PAS-seq.b1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d45.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d45.PAS-seq.b2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d50.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d50.PAS-seq.b1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d50.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d50.PAS-seq.b2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d55.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d55.PAS-seq.b1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d55.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d55.PAS-seq.b2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d60.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d60.PAS-seq.b1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d60.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d60.PAS-seq.b2 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d00.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d00.PAS-seq.b1.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d00.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d00.PAS-seq.b2.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d05.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d05.PAS-seq.b1.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d05.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d05.PAS-seq.b2.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d10.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d10.PAS-seq.b1.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d10.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d10.PAS-seq.b2.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d15.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d15.PAS-seq.b1.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d15.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d15.PAS-seq.b2.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d20.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d20.PAS-seq.b1.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d20.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d20.PAS-seq.b2.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d25.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d25.PAS-seq.b1.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d25.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d25.PAS-seq.b2.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d30.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d30.PAS-seq.b1.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d30.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d30.PAS-seq.b2.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d35.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d35.PAS-seq.b1.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d35.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d35.PAS-seq.b2.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d40.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d40.PAS-seq.b1.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d40.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d40.PAS-seq.b2.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d45.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d45.PAS-seq.b1.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d45.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d45.PAS-seq.b2.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d50.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d50.PAS-seq.b1.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d50.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d50.PAS-seq.b2.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d55.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d55.PAS-seq.b1.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d55.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d55.PAS-seq.b2.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d60.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d60.PAS-seq.b1.dedup -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes4_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf primary_keratinocyte-d60.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes sam_reads_in_genes-primary_keratinocyte-d60.PAS-seq.b2.dedup -nomulti