python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py EMX1.1-transient-IP-SRR1168390.1x36mers.hg38-male.unique.MACS-2.1.0_peaks.narrowPeak.gz 0 EMX1.1-transient-IP-SRR1168390.1x36mers.hg38-male.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes EMX1.1-transient-IP-SRR1168390.1x36mers.hg38-male.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py EMX1.3-transient-IP-SRR1168391.1x36mers.hg38-male.unique.MACS-2.1.0_peaks.narrowPeak.gz 0 EMX1.3-transient-IP-SRR1168391.1x36mers.hg38-male.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes EMX1.3-transient-IP-SRR1168391.1x36mers.hg38-male.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Nanog-sg2-10ug-IP-SRR1168389.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.gz 0 Nanog-sg2-10ug-IP-SRR1168389.1x36mers.mm10.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes Nanog-sg2-10ug-IP-SRR1168389.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Nanog-sg2-40ug-IP-SRR1168388.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.gz 0 Nanog-sg2-40ug-IP-SRR1168388.1x36mers.mm10.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes Nanog-sg2-40ug-IP-SRR1168388.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Nanog-sg2-IP-SRR1163498.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.gz 0 Nanog-sg2-IP-SRR1163498.1x36mers.mm10.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes Nanog-sg2-IP-SRR1163498.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Nanog-sg3-0.02ug-IP-SRR1168387.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.gz 0 Nanog-sg3-0.02ug-IP-SRR1168387.1x36mers.mm10.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes Nanog-sg3-0.02ug-IP-SRR1168387.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Nanog-sg3-0.2ug-IP-SRR1168386.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.gz 0 Nanog-sg3-0.2ug-IP-SRR1168386.1x36mers.mm10.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes Nanog-sg3-0.2ug-IP-SRR1168386.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Nanog-sg3-20ug-IP-SRR1168384.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.gz 0 Nanog-sg3-20ug-IP-SRR1168384.1x36mers.mm10.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes Nanog-sg3-20ug-IP-SRR1168384.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Nanog-sg3-2ug-IP-SRR1168385.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.gz 0 Nanog-sg3-2ug-IP-SRR1168385.1x36mers.mm10.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes Nanog-sg3-2ug-IP-SRR1168385.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Nanog-sg3-IP-SRR1163499.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.gz 0 Nanog-sg3-IP-SRR1163499.1x36mers.mm10.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes Nanog-sg3-IP-SRR1163499.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Nanog-sg3-transient-Input-SRR1168383.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.gz 0 Nanog-sg3-transient-Input-SRR1168383.1x36mers.mm10.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes Nanog-sg3-transient-Input-SRR1168383.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Nanog-sg3-transient-IP-SRR1168382.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.gz 0 Nanog-sg3-transient-IP-SRR1168382.1x36mers.mm10.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes Nanog-sg3-transient-IP-SRR1168382.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Phc1-sg1-IP-SRR1163496.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.gz 0 Phc1-sg1-IP-SRR1163496.1x36mers.mm10.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes Phc1-sg1-IP-SRR1163496.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py Phc1-sg2-IP-SRR1163497.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.gz 0 Phc1-sg2-IP-SRR1163497.1x36mers.mm10.unique.bam /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes Phc1-sg2-IP-SRR1163497.1x36mers.mm10.unique.MACS-2.1.0_peaks.narrowPeak.RPM -RPM -printSum -uniqueBAM &