python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL49_b3_RNA_kidney.T108_b3_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL49_b3_RNA_kidney.T108_b3_Kidney_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL50_b3_RNA_kidney.T108_b3_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL50_b3_RNA_kidney.T108_b3_Kidney_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL52_b3_RNA_kidney.T108_b3_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL52_b3_RNA_kidney.T108_b3_Kidney_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL54_b3_RNA_kidney.T108_b3_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL54_b3_RNA_kidney.T108_b3_Kidney_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL55_b3_RNA_kidney.T108_b3_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL55_b3_RNA_kidney.T108_b3_Kidney_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL56_b3_RNA_kidney.T108_b3_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL56_b3_RNA_kidney.T108_b3_Kidney_PCW17 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL49_b3_RNA_kidney.T181_b3_Kidney_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL49_b3_RNA_kidney.T181_b3_Kidney_PCW19 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL50_b3_RNA_kidney.T181_b3_Kidney_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL50_b3_RNA_kidney.T181_b3_Kidney_PCW19 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL52_b3_RNA_kidney.T181_b3_Kidney_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL52_b3_RNA_kidney.T181_b3_Kidney_PCW19 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL54_b3_RNA_kidney.T181_b3_Kidney_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL54_b3_RNA_kidney.T181_b3_Kidney_PCW19 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL55_b3_RNA_kidney.T181_b3_Kidney_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL55_b3_RNA_kidney.T181_b3_Kidney_PCW19 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL56_b3_RNA_kidney.T181_b3_Kidney_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL56_b3_RNA_kidney.T181_b3_Kidney_PCW19 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL49_b3_RNA_kidney.T284_b3_Kidney_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL49_b3_RNA_kidney.T284_b3_Kidney_PCW14 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL50_b3_RNA_kidney.T284_b3_Kidney_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL50_b3_RNA_kidney.T284_b3_Kidney_PCW14 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL52_b3_RNA_kidney.T284_b3_Kidney_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL52_b3_RNA_kidney.T284_b3_Kidney_PCW14 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL54_b3_RNA_kidney.T284_b3_Kidney_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL54_b3_RNA_kidney.T284_b3_Kidney_PCW14 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL55_b3_RNA_kidney.T284_b3_Kidney_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL55_b3_RNA_kidney.T284_b3_Kidney_PCW14 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL56_b3_RNA_kidney.T284_b3_Kidney_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL56_b3_RNA_kidney.T284_b3_Kidney_PCW14 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL49_b3_RNA_kidney.T309_b3_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL49_b3_RNA_kidney.T309_b3_Kidney_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL50_b3_RNA_kidney.T309_b3_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL50_b3_RNA_kidney.T309_b3_Kidney_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL52_b3_RNA_kidney.T309_b3_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL52_b3_RNA_kidney.T309_b3_Kidney_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL54_b3_RNA_kidney.T309_b3_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL54_b3_RNA_kidney.T309_b3_Kidney_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL55_b3_RNA_kidney.T309_b3_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL55_b3_RNA_kidney.T309_b3_Kidney_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL56_b3_RNA_kidney.T309_b3_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL56_b3_RNA_kidney.T309_b3_Kidney_PCW21 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL49_b3_RNA_kidney.T359_b3_Kidney_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL49_b3_RNA_kidney.T359_b3_Kidney_PCW20 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL50_b3_RNA_kidney.T359_b3_Kidney_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL50_b3_RNA_kidney.T359_b3_Kidney_PCW20 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL52_b3_RNA_kidney.T359_b3_Kidney_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL52_b3_RNA_kidney.T359_b3_Kidney_PCW20 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL54_b3_RNA_kidney.T359_b3_Kidney_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL54_b3_RNA_kidney.T359_b3_Kidney_PCW20 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL55_b3_RNA_kidney.T359_b3_Kidney_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL55_b3_RNA_kidney.T359_b3_Kidney_PCW20 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL56_b3_RNA_kidney.T359_b3_Kidney_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL56_b3_RNA_kidney.T359_b3_Kidney_PCW20 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL49_b3_RNA_kidney.T373_b3_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL49_b3_RNA_kidney.T373_b3_Kidney_PCW15 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL50_b3_RNA_kidney.T373_b3_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL50_b3_RNA_kidney.T373_b3_Kidney_PCW15 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL52_b3_RNA_kidney.T373_b3_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL52_b3_RNA_kidney.T373_b3_Kidney_PCW15 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL54_b3_RNA_kidney.T373_b3_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL54_b3_RNA_kidney.T373_b3_Kidney_PCW15 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL55_b3_RNA_kidney.T373_b3_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL55_b3_RNA_kidney.T373_b3_Kidney_PCW15 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL56_b3_RNA_kidney.T373_b3_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL56_b3_RNA_kidney.T373_b3_Kidney_PCW15 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL49_b3_RNA_kidney.T389_b3_Kidney_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL49_b3_RNA_kidney.T389_b3_Kidney_PCW13 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL50_b3_RNA_kidney.T389_b3_Kidney_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL50_b3_RNA_kidney.T389_b3_Kidney_PCW13 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL52_b3_RNA_kidney.T389_b3_Kidney_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL52_b3_RNA_kidney.T389_b3_Kidney_PCW13 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL54_b3_RNA_kidney.T389_b3_Kidney_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL54_b3_RNA_kidney.T389_b3_Kidney_PCW13 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL55_b3_RNA_kidney.T389_b3_Kidney_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL55_b3_RNA_kidney.T389_b3_Kidney_PCW13 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL56_b3_RNA_kidney.T389_b3_Kidney_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL56_b3_RNA_kidney.T389_b3_Kidney_PCW13 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL49_b3_RNA_kidney.T65_b3_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL49_b3_RNA_kidney.T65_b3_Kidney_PCW18 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL50_b3_RNA_kidney.T65_b3_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL50_b3_RNA_kidney.T65_b3_Kidney_PCW18 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL52_b3_RNA_kidney.T65_b3_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL52_b3_RNA_kidney.T65_b3_Kidney_PCW18 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL54_b3_RNA_kidney.T65_b3_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL54_b3_RNA_kidney.T65_b3_Kidney_PCW18 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL55_b3_RNA_kidney.T65_b3_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL55_b3_RNA_kidney.T65_b3_Kidney_PCW18 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.gtf SL56_b3_RNA_kidney.T65_b3_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes sam_reads_genes-SL56_b3_RNA_kidney.T65_b3_Kidney_PCW18 -nomulti &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL49_b3_RNA_kidney.T108_b3_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL49_b3_RNA_kidney.T108_b3_Kidney_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL50_b3_RNA_kidney.T108_b3_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL50_b3_RNA_kidney.T108_b3_Kidney_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL52_b3_RNA_kidney.T108_b3_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL52_b3_RNA_kidney.T108_b3_Kidney_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL54_b3_RNA_kidney.T108_b3_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL54_b3_RNA_kidney.T108_b3_Kidney_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL55_b3_RNA_kidney.T108_b3_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL55_b3_RNA_kidney.T108_b3_Kidney_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL56_b3_RNA_kidney.T108_b3_Kidney_PCW17.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL56_b3_RNA_kidney.T108_b3_Kidney_PCW17 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL49_b3_RNA_kidney.T181_b3_Kidney_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL49_b3_RNA_kidney.T181_b3_Kidney_PCW19 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL50_b3_RNA_kidney.T181_b3_Kidney_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL50_b3_RNA_kidney.T181_b3_Kidney_PCW19 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL52_b3_RNA_kidney.T181_b3_Kidney_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL52_b3_RNA_kidney.T181_b3_Kidney_PCW19 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL54_b3_RNA_kidney.T181_b3_Kidney_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL54_b3_RNA_kidney.T181_b3_Kidney_PCW19 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL55_b3_RNA_kidney.T181_b3_Kidney_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL55_b3_RNA_kidney.T181_b3_Kidney_PCW19 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL56_b3_RNA_kidney.T181_b3_Kidney_PCW19.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL56_b3_RNA_kidney.T181_b3_Kidney_PCW19 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL49_b3_RNA_kidney.T284_b3_Kidney_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL49_b3_RNA_kidney.T284_b3_Kidney_PCW14 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL50_b3_RNA_kidney.T284_b3_Kidney_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL50_b3_RNA_kidney.T284_b3_Kidney_PCW14 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL52_b3_RNA_kidney.T284_b3_Kidney_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL52_b3_RNA_kidney.T284_b3_Kidney_PCW14 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL54_b3_RNA_kidney.T284_b3_Kidney_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL54_b3_RNA_kidney.T284_b3_Kidney_PCW14 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL55_b3_RNA_kidney.T284_b3_Kidney_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL55_b3_RNA_kidney.T284_b3_Kidney_PCW14 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL56_b3_RNA_kidney.T284_b3_Kidney_PCW14.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL56_b3_RNA_kidney.T284_b3_Kidney_PCW14 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL49_b3_RNA_kidney.T309_b3_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL49_b3_RNA_kidney.T309_b3_Kidney_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL50_b3_RNA_kidney.T309_b3_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL50_b3_RNA_kidney.T309_b3_Kidney_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL52_b3_RNA_kidney.T309_b3_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL52_b3_RNA_kidney.T309_b3_Kidney_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL54_b3_RNA_kidney.T309_b3_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL54_b3_RNA_kidney.T309_b3_Kidney_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL55_b3_RNA_kidney.T309_b3_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL55_b3_RNA_kidney.T309_b3_Kidney_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL56_b3_RNA_kidney.T309_b3_Kidney_PCW21.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL56_b3_RNA_kidney.T309_b3_Kidney_PCW21 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL49_b3_RNA_kidney.T359_b3_Kidney_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL49_b3_RNA_kidney.T359_b3_Kidney_PCW20 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL50_b3_RNA_kidney.T359_b3_Kidney_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL50_b3_RNA_kidney.T359_b3_Kidney_PCW20 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL52_b3_RNA_kidney.T359_b3_Kidney_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL52_b3_RNA_kidney.T359_b3_Kidney_PCW20 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL54_b3_RNA_kidney.T359_b3_Kidney_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL54_b3_RNA_kidney.T359_b3_Kidney_PCW20 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL55_b3_RNA_kidney.T359_b3_Kidney_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL55_b3_RNA_kidney.T359_b3_Kidney_PCW20 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL56_b3_RNA_kidney.T359_b3_Kidney_PCW20.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL56_b3_RNA_kidney.T359_b3_Kidney_PCW20 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL49_b3_RNA_kidney.T373_b3_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL49_b3_RNA_kidney.T373_b3_Kidney_PCW15 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL50_b3_RNA_kidney.T373_b3_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL50_b3_RNA_kidney.T373_b3_Kidney_PCW15 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL52_b3_RNA_kidney.T373_b3_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL52_b3_RNA_kidney.T373_b3_Kidney_PCW15 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL54_b3_RNA_kidney.T373_b3_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL54_b3_RNA_kidney.T373_b3_Kidney_PCW15 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL55_b3_RNA_kidney.T373_b3_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL55_b3_RNA_kidney.T373_b3_Kidney_PCW15 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL56_b3_RNA_kidney.T373_b3_Kidney_PCW15.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL56_b3_RNA_kidney.T373_b3_Kidney_PCW15 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL49_b3_RNA_kidney.T389_b3_Kidney_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL49_b3_RNA_kidney.T389_b3_Kidney_PCW13 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL50_b3_RNA_kidney.T389_b3_Kidney_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL50_b3_RNA_kidney.T389_b3_Kidney_PCW13 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL52_b3_RNA_kidney.T389_b3_Kidney_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL52_b3_RNA_kidney.T389_b3_Kidney_PCW13 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL54_b3_RNA_kidney.T389_b3_Kidney_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL54_b3_RNA_kidney.T389_b3_Kidney_PCW13 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL55_b3_RNA_kidney.T389_b3_Kidney_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL55_b3_RNA_kidney.T389_b3_Kidney_PCW13 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL56_b3_RNA_kidney.T389_b3_Kidney_PCW13.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL56_b3_RNA_kidney.T389_b3_Kidney_PCW13 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL49_b3_RNA_kidney.T65_b3_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL49_b3_RNA_kidney.T65_b3_Kidney_PCW18 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL50_b3_RNA_kidney.T65_b3_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL50_b3_RNA_kidney.T65_b3_Kidney_PCW18 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL52_b3_RNA_kidney.T65_b3_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL52_b3_RNA_kidney.T65_b3_Kidney_PCW18 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL54_b3_RNA_kidney.T65_b3_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL54_b3_RNA_kidney.T65_b3_Kidney_PCW18 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL55_b3_RNA_kidney.T65_b3_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL55_b3_RNA_kidney.T65_b3_Kidney_PCW18 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL56_b3_RNA_kidney.T65_b3_Kidney_PCW18.end1.hg38-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam SAMstats-SL56_b3_RNA_kidney.T65_b3_Kidney_PCW18 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools