python ~/code/bedRPKMfromBAM.py ChCUC1_halo_REP1.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ChCUC1_halo_REP1.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes ChCUC1_halo_REP1.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ChCUC1_halo_REP2.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ChCUC1_halo_REP2.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes ChCUC1_halo_REP2.SE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py ChCUC1_halo_REP3.SE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 ChCUC1_halo_REP3.SE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Cardamine_hirsuta-ddCarHirs1.hap2.1/Cardamine_hirsuta-ddCarHirs1.hap2.1.chrom.sizes ChCUC1_halo_REP3.SE.a.MACS-2.1.0_peaks.RPM -RPM