python ~/code/bedRPKMfromBAM.py DAP_BAF60.21_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_BAF60.21_deM_SE50.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 DAP_BAF60.21_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_BSD8_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_BSD8_deM_SE50.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 DAP_BSD8_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_bZIP76_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_bZIP76_deM_SE50.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 DAP_bZIP76_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_C3H42_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_C3H42_deM_SE50.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 DAP_C3H42_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_CAP5P9_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_CAP5P9_deM_SE50.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 DAP_CAP5P9_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_CPP8_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_CPP8_deM_SE50.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 DAP_CPP8_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_DOF23_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_DOF23_deM_SE50.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 DAP_DOF23_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_DOF3_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_DOF3_deM_SE50.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 DAP_DOF3_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_E2F19_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_E2F19_deM_SE50.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 DAP_E2F19_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_EREB122_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_EREB122_deM_SE50.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 DAP_EREB122_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_EREB156_Met_SE150_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_EREB156_Met_SE150_SE50.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 DAP_EREB156_Met_SE150_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_EREB7_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_EREB7_deM_SE50.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 DAP_EREB7_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_GBP20_Met_SE150.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_GBP20_Met_SE150.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 DAP_GBP20_Met_SE150.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_HSF24_Met_SE150_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_HSF24_Met_SE150_SE50.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 DAP_HSF24_Met_SE150_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_JMJ13_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_JMJ13_deM_SE50.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 DAP_JMJ13_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_MBF1.3_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_MBF1.3_deM_SE50.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 DAP_MBF1.3_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_MYB100_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_MYB100_deM_SE50.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 DAP_MYB100_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_MYB40_Met_SE150_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_MYB40_Met_SE150_SE50.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 DAP_MYB40_Met_SE150_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_MYB53_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_MYB53_deM_SE50.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 DAP_MYB53_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_MYBR78_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_MYBR78_deM_SE50.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 DAP_MYBR78_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_NAC102_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_NAC102_deM_SE50.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 DAP_NAC102_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_NLP14_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_NLP14_deM_SE50.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 DAP_NLP14_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_Orphan175_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_Orphan175_deM_SE50.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 DAP_Orphan175_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_Orphan207_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_Orphan207_deM_SE50.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 DAP_Orphan207_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_Orphan249_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_Orphan249_deM_SE50.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 DAP_Orphan249_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_THX39_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_THX39_deM_SE50.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 DAP_THX39_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DAP_WRKY38_deM_SE50.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DAP_WRKY38_deM_SE50.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 DAP_WRKY38_deM_SE50.SE.a.MACS-2.1.0_peaks.RPM -RPM