python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS111-1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS111-1 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS111-2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS111-2 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS111-3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS111-3 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS119-1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS119-1 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS119-2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS119-2 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS119-3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS119-3 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS48-1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS48-1 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS48-2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS48-2 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS48-3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS48-3 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS51-1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS51-1 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS51-2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS51-2 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS51-3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS51-3 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS6-1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS6-1 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS6-2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS6-2 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS6-3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS6-3 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS77-1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS77-1 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS77-2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS77-2 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RPE1-SS77-3-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RPE1-SS77-3 -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes  samtools -paired