python ~/code/bedRPKMfromBAM.py ABI19_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ABI19_B73.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 ABI19_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ABI34_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ABI34_B73.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 ABI34_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ABI8_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ABI8_B73.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 ABI8_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARR5_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARR5_B73.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 ARR5_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BAF1_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BAF1_B73.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 BAF1_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH106_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH106_B73.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 BHLH106_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH113_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH113_B73.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 BHLH113_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH125_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH125_B73.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 BHLH125_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH135_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH135_B73.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 BHLH135_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH149_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH149_B73.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 BHLH149_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH14_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH14_B73.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 BHLH14_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH150_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH150_B73.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 BHLH150_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH168_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH168_B73.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 BHLH168_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH17_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH17_B73.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 BHLH17_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH52_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH52_B73.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 BHLH52_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH57_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH57_B73.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 BHLH57_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH61_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH61_B73.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 BHLH61_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH67_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH67_B73.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 BHLH67_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH85_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH85_B73.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 BHLH85_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH91_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH91_B73.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 BHLH91_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH99_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH99_B73.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 BHLH99_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP105_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP105_B73.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 BZIP105_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP106_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP106_B73.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 BZIP106_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP111_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP111_B73.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 BZIP111_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP112_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP112_B73.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 BZIP112_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP115_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP115_B73.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 BZIP115_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP124_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP124_B73.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 BZIP124_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP128_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP128_B73.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 BZIP128_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP12_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP12_B73.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 BZIP12_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP13_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP13_B73.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 BZIP13_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP160_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP160_B73.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 BZIP160_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP1_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP1_B73.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 BZIP1_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP21_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP21_B73.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 BZIP21_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP23_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP23_B73.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 BZIP23_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP25_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP25_B73.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 BZIP25_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP27_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP27_B73.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 BZIP27_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP2_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP2_B73.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 BZIP2_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP34_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP34_B73.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 BZIP34_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP39_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP39_B73.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 BZIP39_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP40_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP40_B73.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 BZIP40_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP41_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP41_B73.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 BZIP41_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP48_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP48_B73.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_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP52_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP52_B73.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 BZIP52_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP54_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP54_B73.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 BZIP54_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP58_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP58_B73.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_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP61_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP61_B73.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 BZIP61_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP62_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP62_B73.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 BZIP62_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP68_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP68_B73.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 BZIP68_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP70_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP70_B73.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 BZIP70_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP79_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP79_B73.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 BZIP79_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP84_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP84_B73.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 BZIP84_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP86_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP86_B73.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 BZIP86_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP87_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP87_B73.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 BZIP87_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP90_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP90_B73.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 BZIP90_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP91_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP91_B73.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 BZIP91_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP92_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP92_B73.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_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP94_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP94_B73.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 BZIP94_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP99_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP99_B73.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 BZIP99_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZR1_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZR1_B73.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 BZR1_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py CA2P13_CA3P1_CA5P7_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 CA2P13_CA3P1_CA5P7_B73.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 CA2P13_CA3P1_CA5P7_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py CA2P13_CA3P4_CA5P7_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 CA2P13_CA3P4_CA5P7_B73.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 CA2P13_CA3P4_CA5P7_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py CCHH2_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 CCHH2_B73.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 CCHH2_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH113_BHLH125_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH113_BHLH125_B73.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 DD_BHLH113_BHLH125_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH113_BHLH168_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH113_BHLH168_B73.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 DD_BHLH113_BHLH168_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH135_BHLH125_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH135_BHLH125_B73.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 DD_BHLH135_BHLH125_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH135_BHLH168_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH135_BHLH168_B73.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 DD_BHLH135_BHLH168_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH14_BHLH125_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH14_BHLH125_B73.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 DD_BHLH14_BHLH125_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH14_BHLH168_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH14_BHLH168_B73.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 DD_BHLH14_BHLH168_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH150_BHLH125_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH150_BHLH125_B73.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 DD_BHLH150_BHLH125_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH150_BHLH168_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH150_BHLH168_B73.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 DD_BHLH150_BHLH168_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH52_BHLH125_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH52_BHLH125_B73.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 DD_BHLH52_BHLH125_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH52_BHLH168_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH52_BHLH168_B73.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 DD_BHLH52_BHLH168_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH61_BHLH125_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH61_BHLH125_B73.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 DD_BHLH61_BHLH125_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH61_BHLH168_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH61_BHLH168_B73.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 DD_BHLH61_BHLH168_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH67_BHLH125_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH67_BHLH125_B73.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 DD_BHLH67_BHLH125_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH67_BHLH168_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH67_BHLH168_B73.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 DD_BHLH67_BHLH168_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH85_BHLH125_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH85_BHLH125_B73.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 DD_BHLH85_BHLH125_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH85_BHLH168_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH85_BHLH168_B73.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 DD_BHLH85_BHLH168_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH92_BHLH125_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH92_BHLH125_B73.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 DD_BHLH92_BHLH125_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH92_BHLH168_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH92_BHLH168_B73.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 DD_BHLH92_BHLH168_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DOF1_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DOF1_B73.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 DOF1_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DOF24_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DOF24_B73.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 DOF24_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB126_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB126_B73.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 EREB126_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB145_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB145_B73.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 EREB145_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB149_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB149_B73.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 EREB149_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB183_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB183_B73.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 EREB183_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB201_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB201_B73.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 EREB201_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB2_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB2_B73.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 EREB2_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB36_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB36_B73.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 EREB36_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB46_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB46_B73.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 EREB46_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB49_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB49_B73.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 EREB49_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB4_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB4_B73.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 EREB4_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB53_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB53_B73.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 EREB53_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB87_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB87_B73.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 EREB87_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GATA20_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GATA20_B73.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 GATA20_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GBP10_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GBP10_B73.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 GBP10_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GBP11_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GBP11_B73.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 GBP11_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GBP4_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GBP4_B73.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 GBP4_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK17_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK17_B73.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 GLK17_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK20_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK20_B73.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 GLK20_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK21_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK21_B73.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 GLK21_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK44_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK44_B73.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 GLK44_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK47_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK47_B73.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 GLK47_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK48_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK48_B73.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 GLK48_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK53_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK53_B73.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 GLK53_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK56_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK56_B73.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 GLK56_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GRF2_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GRF2_B73.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 GRF2_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GRF3_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GRF3_B73.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 GRF3_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GRF6_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GRF6_B73.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 GRF6_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GRF7_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GRF7_B73.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 GRF7_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GRF9_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GRF9_B73.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 GRF9_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB102_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB102_B73.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 HB102_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB117_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB117_B73.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 HB117_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB122_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB122_B73.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 HB122_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB125_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB125_B73.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 HB125_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB15_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB15_B73.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 HB15_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB22_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB22_B73.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 HB22_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB54_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB54_B73.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 HB54_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB67_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB67_B73.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 HB67_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB68_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB68_B73.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 HB68_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HSF10_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HSF10_B73.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 HSF10_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HSF24_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HSF24_B73.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 HSF24_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HSF25_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HSF25_B73.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 HSF25_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HSF7_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HSF7_B73.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 HSF7_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py LBD37_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 LBD37_B73.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 LBD37_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MADS12_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MADS12_B73.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 MADS12_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MADS43_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MADS43_B73.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 MADS43_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MADS68_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MADS68_B73.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 MADS68_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MADS69_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MADS69_B73.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 MADS69_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MADS72_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MADS72_B73.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 MADS72_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MADS73_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MADS73_B73.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 MADS73_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB131_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB131_B73.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 MYB131_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB138_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB138_B73.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 MYB138_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB40_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB40_B73.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 MYB40_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB50_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB50_B73.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 MYB50_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB73_DED1_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB73_DED1_Mo17.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 MYB73_DED1_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB83_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB83_B73.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 MYB83_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR101_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR101_B73.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 MYBR101_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR111_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR111_B73.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 MYBR111_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR17_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR17_B73.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 MYBR17_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR52_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR52_B73.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 MYBR52_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR58_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR58_B73.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 MYBR58_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC115_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC115_B73.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 NAC115_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC116_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC116_B73.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 NAC116_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC12_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC12_B73.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 NAC12_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC20_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC20_B73.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 NAC20_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC25_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC25_B73.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 NAC25_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC27_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC27_B73.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 NAC27_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC28_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC28_B73.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 NAC28_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC33_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC33_B73.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 NAC33_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC3_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC3_B73.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 NAC3_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC42_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC42_B73.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 NAC42_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC49_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC49_B73.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 NAC49_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC71_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC71_B73.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 NAC71_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC74_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC74_B73.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 NAC74_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC86_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC86_B73.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 NAC86_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NFYA1_LEC1_CA5P16_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NFYA1_LEC1_CA5P16_B73.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 NFYA1_LEC1_CA5P16_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NKD1_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NKD1_B73.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 NKD1_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NKD2_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NKD2_B73.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 NKD2_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NLP14_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NLP14_B73.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 NLP14_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py SBP15_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 SBP15_B73.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 SBP15_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py SBP1_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 SBP1_B73.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 SBP1_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py SBP2_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 SBP2_B73.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 SBP2_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py SBP30_rep1_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 SBP30_rep1_B73.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 SBP30_rep1_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py SBP30_rep2_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 SBP30_rep2_B73.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 SBP30_rep2_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py SBP32_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 SBP32_B73.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 SBP32_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP11_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP11_B73.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 TCP11_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP15_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP15_B73.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 TCP15_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP2_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP2_B73.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 TCP2_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP30_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP30_B73.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 TCP30_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP4_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP4_B73.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 TCP4_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP5_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP5_B73.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 TCP5_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP8_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP8_B73.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 TCP8_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py THX16_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 THX16_B73.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 THX16_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py THX20_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 THX20_B73.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 THX20_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py THX26_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 THX26_B73.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 THX26_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py WRKY11_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 WRKY11_B73.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 WRKY11_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py WRKY125_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 WRKY125_B73.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 WRKY125_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py WRKY53_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 WRKY53_B73.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_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py WRKY57_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 WRKY57_B73.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 WRKY57_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py WRKY64_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 WRKY64_B73.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 WRKY64_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py WRKY82_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 WRKY82_B73.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 WRKY82_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py YAB2_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 YAB2_B73.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 YAB2_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZHD15_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZHD15_B73.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 ZHD15_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZHD1_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZHD1_B73.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 ZHD1_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZHD21_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZHD21_B73.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 ZHD21_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZHD4_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZHD4_B73.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 ZHD4_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZHD5_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZHD5_B73.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 ZHD5_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZIM2_B73.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZIM2_B73.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 ZIM2_B73.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ABI19_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ABI19_Mo17.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 ABI19_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ABI34_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ABI34_Mo17.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 ABI34_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ABI8_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ABI8_Mo17.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 ABI8_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARF10_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARF10_Mo17.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 ARF10_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARF13_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARF13_Mo17.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 ARF13_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARF14_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARF14_Mo17.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 ARF14_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARF16_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARF16_Mo17.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 ARF16_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARF18_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARF18_Mo17.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 ARF18_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARF25_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARF25_Mo17.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 ARF25_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARF27_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARF27_Mo17.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 ARF27_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARF29_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARF29_Mo17.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 ARF29_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARF34_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARF34_Mo17.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 ARF34_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARF35_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARF35_Mo17.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 ARF35_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARF36_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARF36_Mo17.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 ARF36_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARF39_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARF39_Mo17.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 ARF39_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARF4_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARF4_Mo17.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 ARF4_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARF7_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARF7_Mo17.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 ARF7_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ARR5_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ARR5_Mo17.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 ARR5_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BAF1_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BAF1_Mo17.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 BAF1_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BAFL12_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BAFL12_Mo17.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 BAFL12_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BAFL3_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BAFL3_Mo17.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 BAFL3_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH106_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH106_Mo17.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 BHLH106_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH113_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH113_Mo17.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 BHLH113_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH125_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH125_Mo17.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 BHLH125_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH135_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH135_Mo17.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 BHLH135_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH149_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH149_Mo17.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 BHLH149_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH150_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH150_Mo17.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 BHLH150_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH168_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH168_Mo17.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 BHLH168_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH17_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH17_Mo17.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 BHLH17_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH52_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH52_Mo17.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 BHLH52_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH57_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH57_Mo17.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 BHLH57_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH61_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH61_Mo17.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 BHLH61_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH67_BA1_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH67_BA1_Mo17.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 BHLH67_BA1_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH85_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH85_Mo17.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 BHLH85_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH91_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH91_Mo17.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 BHLH91_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BHLH99_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BHLH99_Mo17.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 BHLH99_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP105_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP105_Mo17.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 BZIP105_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP106_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP106_Mo17.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 BZIP106_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP111_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP111_Mo17.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 BZIP111_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP112_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP112_Mo17.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 BZIP112_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP115_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP115_Mo17.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 BZIP115_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP124_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP124_Mo17.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 BZIP124_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP128_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP128_Mo17.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 BZIP128_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP12_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP12_Mo17.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 BZIP12_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP13_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP13_Mo17.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 BZIP13_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP160_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP160_Mo17.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 BZIP160_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP1_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP1_Mo17.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 BZIP1_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP21_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP21_Mo17.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 BZIP21_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP23_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP23_Mo17.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 BZIP23_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP25_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP25_Mo17.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 BZIP25_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP27_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP27_Mo17.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 BZIP27_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP2_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP2_Mo17.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 BZIP2_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP34_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP34_Mo17.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 BZIP34_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP39_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP39_Mo17.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 BZIP39_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP40_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP40_Mo17.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 BZIP40_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP41_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP41_Mo17.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 BZIP41_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP48_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP48_Mo17.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_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP52_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP52_Mo17.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 BZIP52_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP54_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP54_Mo17.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 BZIP54_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP57_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP57_Mo17.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 BZIP57_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP58_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP58_Mo17.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_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP61_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP61_Mo17.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 BZIP61_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP62_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP62_Mo17.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 BZIP62_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP68_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP68_Mo17.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 BZIP68_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP70_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP70_Mo17.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 BZIP70_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP72_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP72_Mo17.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 BZIP72_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP79_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP79_Mo17.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 BZIP79_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP84_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP84_Mo17.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 BZIP84_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP86_rep1_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP86_rep1_Mo17.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 BZIP86_rep1_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP86_rep2_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP86_rep2_Mo17.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 BZIP86_rep2_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP87_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP87_Mo17.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 BZIP87_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP90_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP90_Mo17.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 BZIP90_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP91_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP91_Mo17.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 BZIP91_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP92_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP92_Mo17.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_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP94_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP94_Mo17.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 BZIP94_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP96_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP96_Mo17.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 BZIP96_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZIP99_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZIP99_Mo17.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 BZIP99_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py BZR1_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 BZR1_Mo17.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 BZR1_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py CA2P13_CA3P1_CA5P7_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 CA2P13_CA3P1_CA5P7_Mo17.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 CA2P13_CA3P1_CA5P7_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py CA2P13_CA3P4_CA5P7_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 CA2P13_CA3P4_CA5P7_Mo17.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 CA2P13_CA3P4_CA5P7_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py CCHH2_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 CCHH2_Mo17.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 CCHH2_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DD_BHLH85_BHLH125_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DD_BHLH85_BHLH125_Mo17.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 DD_BHLH85_BHLH125_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DOF1_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DOF1_Mo17.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 DOF1_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py DOF24_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 DOF24_Mo17.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 DOF24_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB126_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB126_Mo17.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 EREB126_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB138_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB138_Mo17.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 EREB138_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB145_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB145_Mo17.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 EREB145_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB149_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB149_Mo17.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 EREB149_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB183_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB183_Mo17.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 EREB183_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB201_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB201_Mo17.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 EREB201_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB24_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB24_Mo17.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 EREB24_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB29_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB29_Mo17.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 EREB29_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB2_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB2_Mo17.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 EREB2_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB36_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB36_Mo17.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 EREB36_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB46_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB46_Mo17.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 EREB46_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB49_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB49_Mo17.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 EREB49_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB4_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB4_Mo17.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 EREB4_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB53_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB53_Mo17.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 EREB53_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py EREB87_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 EREB87_Mo17.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 EREB87_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GATA20_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GATA20_Mo17.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 GATA20_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GBP10_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GBP10_Mo17.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 GBP10_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GBP11_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GBP11_Mo17.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 GBP11_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GBP4_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GBP4_Mo17.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 GBP4_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK17_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK17_Mo17.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 GLK17_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK20_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK20_Mo17.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 GLK20_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK21_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK21_Mo17.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 GLK21_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK44_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK44_Mo17.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 GLK44_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK47_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK47_Mo17.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 GLK47_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK48_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK48_Mo17.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 GLK48_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK53_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK53_Mo17.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 GLK53_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GLK56_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GLK56_Mo17.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 GLK56_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GRF2_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GRF2_Mo17.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 GRF2_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GRF3_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GRF3_Mo17.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 GRF3_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GRF6_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GRF6_Mo17.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 GRF6_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GRF7_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GRF7_Mo17.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 GRF7_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py GRF9_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 GRF9_Mo17.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 GRF9_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB102_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB102_Mo17.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 HB102_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB117_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB117_Mo17.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 HB117_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB122_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB122_Mo17.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 HB122_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB15_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB15_Mo17.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 HB15_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB22_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB22_Mo17.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 HB22_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB54_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB54_Mo17.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 HB54_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB67_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB67_Mo17.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 HB67_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HB68_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HB68_Mo17.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 HB68_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HSF10_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HSF10_Mo17.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 HSF10_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HSF24_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HSF24_Mo17.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 HSF24_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HSF25_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HSF25_Mo17.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 HSF25_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py HSF7_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 HSF7_Mo17.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 HSF7_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py LBD16_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 LBD16_Mo17.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 LBD16_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py LBD19_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 LBD19_Mo17.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 LBD19_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py LBD37_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 LBD37_Mo17.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 LBD37_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py LBD5_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 LBD5_Mo17.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 LBD5_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MADS12_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MADS12_Mo17.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 MADS12_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MADS43_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MADS43_Mo17.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 MADS43_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MADS68_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MADS68_Mo17.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 MADS68_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MADS69_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MADS69_Mo17.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 MADS69_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MADS72_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MADS72_Mo17.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 MADS72_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MADS73_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MADS73_Mo17.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 MADS73_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB131_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB131_Mo17.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 MYB131_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB138_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB138_Mo17.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 MYB138_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB40_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB40_Mo17.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 MYB40_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB50_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB50_Mo17.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 MYB50_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB83_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB83_Mo17.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 MYB83_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYB94_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYB94_Mo17.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 MYB94_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR101_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR101_Mo17.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 MYBR101_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR111_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR111_Mo17.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 MYBR111_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR17_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR17_Mo17.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 MYBR17_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR52_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR52_Mo17.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 MYBR52_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MYBR58_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MYBR58_Mo17.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 MYBR58_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC115_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC115_Mo17.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 NAC115_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC116_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC116_Mo17.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 NAC116_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC12_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC12_Mo17.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 NAC12_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC20_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC20_Mo17.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 NAC20_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC25_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC25_Mo17.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 NAC25_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC27_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC27_Mo17.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 NAC27_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC28_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC28_Mo17.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 NAC28_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC33_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC33_Mo17.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 NAC33_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC3_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC3_Mo17.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 NAC3_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC42_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC42_Mo17.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 NAC42_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC49_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC49_Mo17.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 NAC49_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC71_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC71_Mo17.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 NAC71_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC74_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC74_Mo17.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 NAC74_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC86_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC86_Mo17.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 NAC86_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NAC91_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NAC91_Mo17.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 NAC91_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NFYA1_LEC1_CA5P16_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NFYA1_LEC1_CA5P16_Mo17.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 NFYA1_LEC1_CA5P16_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NKD1_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NKD1_Mo17.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 NKD1_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NKD2_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NKD2_Mo17.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 NKD2_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py NLP14_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 NLP14_Mo17.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 NLP14_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py SBP15_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 SBP15_Mo17.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 SBP15_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py SBP1_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 SBP1_Mo17.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 SBP1_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py SBP2_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 SBP2_Mo17.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 SBP2_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py SBP30_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 SBP30_Mo17.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 SBP30_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py SBP32_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 SBP32_Mo17.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 SBP32_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py SBP6_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 SBP6_Mo17.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 SBP6_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py SBP8_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 SBP8_Mo17.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 SBP8_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP11_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP11_Mo17.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 TCP11_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP15_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP15_Mo17.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 TCP15_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP2_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP2_Mo17.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 TCP2_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP30_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP30_Mo17.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 TCP30_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP3_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP3_Mo17.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 TCP3_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP4_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP4_Mo17.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 TCP4_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP5_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP5_Mo17.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 TCP5_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py TCP8_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 TCP8_Mo17.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 TCP8_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py THX16_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 THX16_Mo17.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 THX16_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py THX20_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 THX20_Mo17.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 THX20_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py THX26_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 THX26_Mo17.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 THX26_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py WRKY11_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 WRKY11_Mo17.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 WRKY11_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py WRKY125_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 WRKY125_Mo17.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 WRKY125_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py WRKY53_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 WRKY53_Mo17.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_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py WRKY57_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 WRKY57_Mo17.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 WRKY57_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py WRKY64_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 WRKY64_Mo17.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 WRKY64_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py WRKY82_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 WRKY82_Mo17.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 WRKY82_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py YAB2_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 YAB2_Mo17.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 YAB2_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZHD15_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZHD15_Mo17.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 ZHD15_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZHD1_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZHD1_Mo17.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 ZHD1_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZHD21_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZHD21_Mo17.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 ZHD21_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZHD4_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZHD4_Mo17.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 ZHD4_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZHD5_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZHD5_Mo17.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 ZHD5_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ZIM2_Mo17.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ZIM2_Mo17.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 ZIM2_Mo17.PE.a.MACS-2.1.0_peaks.RPM -RPM