python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py SK-L001-GM12868-ATAC_50K_cells_1x_PBS_wash-1.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.gz 0 SK-L001-GM12868-ATAC_50K_cells_1x_PBS_wash-1.2x36mers.hg38-female.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  SK-L001-GM12868-ATAC_50K_cells_1x_PBS_wash-1.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py SK-L002-GM12868-ATAC_50K_cells_1x_PBS_wash-2.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.gz 0 SK-L002-GM12868-ATAC_50K_cells_1x_PBS_wash-2.2x36mers.hg38-female.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  SK-L002-GM12868-ATAC_50K_cells_1x_PBS_wash-2.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py SK-L003-GM12868-ATAC_50K_cells_10p_DMSO_1x_PBS_wash-1.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.gz 0 SK-L003-GM12868-ATAC_50K_cells_10p_DMSO_1x_PBS_wash-1.2x36mers.hg38-female.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  SK-L003-GM12868-ATAC_50K_cells_10p_DMSO_1x_PBS_wash-1.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py SK-L004-GM12868-ATAC_50K_cells_10p_DMSO_1x_PBS_wash-2.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.gz 0 SK-L004-GM12868-ATAC_50K_cells_10p_DMSO_1x_PBS_wash-2.2x36mers.hg38-female.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  SK-L004-GM12868-ATAC_50K_cells_10p_DMSO_1x_PBS_wash-2.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py SK-L005-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash-1.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.gz 0 SK-L005-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash-1.2x36mers.hg38-female.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  SK-L005-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash-1.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py SK-L006-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash-2.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.gz 0 SK-L006-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash-2.2x36mers.hg38-female.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  SK-L006-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash-2.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py SK-L007-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_biotin_pulldown-1.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.gz 0 SK-L007-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_biotin_pulldown-1.2x36mers.hg38-female.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  SK-L007-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_biotin_pulldown-1.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py SK-L008-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_biotin_pulldown-2.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.gz 0 SK-L008-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_biotin_pulldown-2.2x36mers.hg38-female.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  SK-L008-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_biotin_pulldown-2.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py SK-L009-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_input-1.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.gz 0 SK-L009-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_input-1.2x36mers.hg38-female.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  SK-L009-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_input-1.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py SK-L010-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_input-2.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.gz 0 SK-L010-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_input-2.2x36mers.hg38-female.unique.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes  SK-L010-GM12868-ATAC_50K_cells_5uM_Kethoxal_1x_PBS_wash_input-2.2x36mers.hg38-female.unique.dedup.MACS2-PE_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM