python ~/code/bedRPKMfromBAM.py ZmARF10-DAP-seq.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZmARF10-DAP-seq.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZmARF10-DAP-seq.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZmARF13-DAP-seq.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZmARF13-DAP-seq.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZmARF13-DAP-seq.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZmARF14-DAP-seq.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZmARF14-DAP-seq.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZmARF14-DAP-seq.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZmARF16-DAP-seq.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZmARF16-DAP-seq.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZmARF16-DAP-seq.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZmARF18-DAP-seq.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZmARF18-DAP-seq.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZmARF18-DAP-seq.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZmARF25-DAP-seq.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZmARF25-DAP-seq.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZmARF25-DAP-seq.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZmARF27-DAP-seq.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZmARF27-DAP-seq.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZmARF27-DAP-seq.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZmARF29-DAP-seq.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZmARF29-DAP-seq.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZmARF29-DAP-seq.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZmARF34-DAP-seq.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZmARF34-DAP-seq.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZmARF34-DAP-seq.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZmARF35-DAP-seq.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZmARF35-DAP-seq.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZmARF35-DAP-seq.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZmARF36-DAP-seq.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZmARF36-DAP-seq.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZmARF36-DAP-seq.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZmARF39-DAP-seq.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZmARF39-DAP-seq.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZmARF39-DAP-seq.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZmARF4-DAP-seq.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZmARF4-DAP-seq.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZmARF4-DAP-seq.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZmARF7-DAP-seq.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZmARF7-DAP-seq.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes ZmARF7-DAP-seq.SE.a.MACS-2.1.0_peaks.RPM -RPM