python ~/code/bedRPKMfromBAM.py 1d030858.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 1d030858.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes 1d030858.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH164.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH164.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BHLH164.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP102.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP102.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP102.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP10.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP10.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP10.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP125.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP125.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP125.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP14.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP14.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP14.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP48.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP48.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP48.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP49.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP49.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP49.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP58.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP58.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP58.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP71.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP71.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP71.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP92.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP92.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes BZIP92.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DOF47.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DOF47.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes DOF47.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB109.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB109.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB109.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB148.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB148.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB148.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB190.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB190.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB190.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB195.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB195.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB195.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB19.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB19.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB19.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB72.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB72.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB72.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB83.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB83.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB83.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB84.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB84.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes EREB84.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB45.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB45.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB45.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB49.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB49.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB49.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB98.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB98.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HB98.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HSFTF20.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HSFTF20.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HSFTF20.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HSFTF5.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HSFTF5.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes HSFTF5.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB127.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB127.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB127.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB32.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB32.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB32.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB35.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB35.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYB35.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR21.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR21.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR21.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR26.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR26.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR26.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR32.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR32.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR32.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR43.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR43.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR43.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR77.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR77.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYBR77.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYC7.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYC7.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes MYC7.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NACTF110.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NACTF110.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NACTF110.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NACTF23.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NACTF23.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NACTF23.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NACTF32.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NACTF32.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NACTF32.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NACTF4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NACTF4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes NACTF4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py O2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 O2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes O2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py OHP1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 OHP1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes OHP1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py THX35.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 THX35.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes THX35.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TU1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TU1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes TU1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py WOX13A.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 WOX13A.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes WOX13A.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py WRKY53.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 WRKY53.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes WRKY53.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py YY1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 YY1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Zea_mays-B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_genomic.chrom.sizes YY1.PE.a.MACS-2.1.0_peaks.RPM -RPM