python ~/code/bedRPKMfromBAM.py Green-APETALA2a.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-APETALA2a.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-APETALA2a.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-ARF4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-ARF4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-ARF4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-BES1_BZR1hp2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-BES1_BZR1hp2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-BES1_BZR1hp2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-BHLH1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-BHLH1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-BHLH1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-CBF2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-CBF2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-CBF2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-CIP2a.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-CIP2a.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-CIP2a.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-cip2b.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-cip2b.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-cip2b.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-CNR.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-CNR.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-CNR.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-CZFP1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-CZFP1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-CZFP1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-Dof4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-Dof4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-Dof4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-DREB3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-DREB3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-DREB3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-EIL1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-EIL1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-EIL1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-EIL2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-EIL2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-EIL2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-EIL3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-EIL3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-EIL3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-EIL4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-EIL4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-EIL4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-ERF10.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-ERF10.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-ERF10.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-ERF9.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-ERF9.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-ERF9.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-GRAS10.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-GRAS10.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-GRAS10.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-GRAS12.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-GRAS12.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-GRAS12.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-GRAS4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-GRAS4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-GRAS4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-gras6.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-gras6.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-gras6.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-JERF1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-JERF1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-JERF1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-LAT61.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-LAT61.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-LAT61.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-LES1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-LES1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-LES1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-LeT12.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-LeT12.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-LeT12.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-LeZIP2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-LeZIP2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-LeZIP2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-LOB1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-LOB1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-LOB1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-LOB38.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-LOB38.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-LOB38.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-LOB42.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-LOB42.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-LOB42.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-LSD1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-LSD1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-LSD1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-MADS1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-MADS1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-MADS1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-MADS-MC.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-MADS-MC.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-MADS-MC.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-MADS-RIN.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-MADS-RIN.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-MADS-RIN.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-MBD5.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-MBD5.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-MBD5.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-MBP7.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-MBP7.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-MBP7.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-NAC6.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-NAC6.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-NAC6.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-NAC-NOR.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-NAC-NOR.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-NAC-NOR.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-NF-YB-3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-NF-YB-3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-NF-YB-3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-PTI4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-PTI4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-PTI4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SCL32-like.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SCL32-like.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SCL32-like.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SEPALLATA3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SEPALLATA3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SEPALLATA3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlBEL1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlBEL1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlBEL1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlbHLH014.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlbHLH014.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlbHLH014.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlbHLH138.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlbHLH138.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlbHLH138.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlbHLH147.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlbHLH147.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlbHLH147.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlC3H11.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlC3H11.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlC3H11.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlC3H48.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlC3H48.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlC3H48.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlCOL1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlCOL1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlCOL1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlDof14.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlDof14.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlDof14.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlDRP1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlDRP1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlDRP1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlERF1a-1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlERF1a-1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlERF1a-1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlERF1a-2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlERF1a-2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlERF1a-2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlERF1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlERF1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlERF1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlERF36.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlERF36.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlERF36.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlERF4-1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlERF4-1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlERF4-1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlERF4-2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlERF4-2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlERF4-2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlERF5-2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlERF5-2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlERF5-2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlERF5.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlERF5.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlERF5.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-Sl-ERF_C_4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-Sl-ERF_C_4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-Sl-ERF_C_4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-Sl-ERF_C_6.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-Sl-ERF_C_6.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-Sl-ERF_C_6.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-Sl-ERF_E_4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-Sl-ERF_E_4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-Sl-ERF_E_4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-Sl-ERF_F_2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-Sl-ERF_F_2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-Sl-ERF_F_2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-Sl-ERF_F_3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-Sl-ERF_F_3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-Sl-ERF_F_3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-Sl-ERF_F_4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-Sl-ERF_F_4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-Sl-ERF_F_4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-Sl-ERF_F_5.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-Sl-ERF_F_5.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-Sl-ERF_F_5.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlGABL2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlGABL2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlGABL2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlGABL4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlGABL4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlGABL4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlGATA9_1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlGATA9_1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlGATA9_1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlGATA9_2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlGATA9_2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlGATA9_2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlGRAS3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlGRAS3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlGRAS3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlGT2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlGT2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlGT2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlHB1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlHB1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlHB1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlHZIP2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlHZIP2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlHZIP2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlHZIP3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlHZIP3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlHZIP3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlMADF1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlMADF1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlMADF1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlMYB44.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlMYB44.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlMYB44.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlMYB70.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlMYB70.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlMYB70.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlMYB91.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlMYB91.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlMYB91.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlMYBL1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlMYBL1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlMYBL1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlMYBL2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlMYBL2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlMYBL2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlMYBL3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlMYBL3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlMYBL3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlMYBL4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlMYBL4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlMYBL4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlNAM1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlNAM1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlNAM1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlNAM2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlNAM2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlNAM2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlNAM3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlNAM3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlNAM3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlNAM4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlNAM4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlNAM4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlNAM5.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlNAM5.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlNAM5.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlTCP12.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlTCP12.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlTCP12.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlTCP15.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlTCP15.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlTCP15.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlTCP18.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlTCP18.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlTCP18.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlWOX14.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlWOX14.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlWOX14.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlWRKY11.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlWRKY11.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlWRKY11.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlWRKY23.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlWRKY23.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlWRKY23.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlWRKY40.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlWRKY40.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlWRKY40.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlWRKY41.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlWRKY41.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlWRKY41.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlWRKY6.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlWRKY6.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlWRKY6.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlWRKY7.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlWRKY7.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlWRKY7.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlWRKY81.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlWRKY81.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlWRKY81.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlYABBY2a.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlYABBY2a.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlYABBY2a.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlZF1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlZF1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlZF1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlZF2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlZF2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlZF2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlZF3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlZF3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlZF3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlZF6.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlZF6.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlZF6.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlZFCL3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlZFCL3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlZFCL3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlZIP1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlZIP1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlZIP1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlZIP3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlZIP3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlZIP3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlZIP4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlZIP4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlZIP4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlZIP5.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlZIP5.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlZIP5.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlZIP6.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlZIP6.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlZIP6.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SlZIP7.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SlZIP7.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SlZIP7.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SolycHsfA2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SolycHsfA2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SolycHsfA2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SolycHsfA4a.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SolycHsfA4a.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SolycHsfA4a.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SolycHsfA6b.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SolycHsfA6b.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SolycHsfA6b.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SolycHsfA7.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SolycHsfA7.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SolycHsfA7.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SolycHsfB1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SolycHsfB1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SolycHsfB1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SolycHsfB2a.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SolycHsfB2a.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SolycHsfB2a.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SolycHsfB2b.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SolycHsfB2b.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SolycHsfB2b.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-SolycHsfC1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-SolycHsfC1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-SolycHsfC1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-TDR4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-TDR4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-TDR4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-TM29.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-TM29.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-TM29.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Green-VAHOX1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Green-VAHOX1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Green-VAHOX1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MBD5-Green-ampDAP_100_B.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MBD5-Green-ampDAP_100_B.end2.fastq.gz.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes MBD5-Green-ampDAP_100_B.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MBD5-Green-ampDAP_150_B.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MBD5-Green-ampDAP_150_B.end2.fastq.gz.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes MBD5-Green-ampDAP_150_B.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MBD5-Green-ampDAP_300_B.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MBD5-Green-ampDAP_300_B.end2.fastq.gz.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes MBD5-Green-ampDAP_300_B.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MBD5-Green-ampDAP_50_B.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MBD5-Green-ampDAP_50_B.end2.fastq.gz.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes MBD5-Green-ampDAP_50_B.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MBD5-Green-DAP_100_D.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MBD5-Green-DAP_100_D.end2.fastq.gz.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes MBD5-Green-DAP_100_D.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MBD5-Green-DAP_150_E.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MBD5-Green-DAP_150_E.end2.fastq.gz.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes MBD5-Green-DAP_150_E.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MBD5-Green-DAP_300_E.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MBD5-Green-DAP_300_E.end2.fastq.gz.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes MBD5-Green-DAP_300_E.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MBD5-Green-DAP_50_E.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MBD5-Green-DAP_50_E.end2.fastq.gz.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes MBD5-Green-DAP_50_E.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MBD5-Red-DAP_100_F.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MBD5-Red-DAP_100_F.end2.fastq.gz.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes MBD5-Red-DAP_100_F.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MBD5-Red-DAP_150_H.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MBD5-Red-DAP_150_H.end2.fastq.gz.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes MBD5-Red-DAP_150_H.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MBD5-Red-DAP_300_H.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MBD5-Red-DAP_300_H.end2.fastq.gz.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes MBD5-Red-DAP_300_H.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py MBD5-Red-DAP_50_H.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 MBD5-Red-DAP_50_H.end2.fastq.gz.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes MBD5-Red-DAP_50_H.end2.fastq.gz.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-APETALA2a.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-APETALA2a.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-APETALA2a.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-ARF4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-ARF4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-ARF4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-BES1_BZR1hp2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-BES1_BZR1hp2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-BES1_BZR1hp2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-BHLH1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-BHLH1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-BHLH1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-CBF2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-CBF2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-CBF2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-CIP2a.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-CIP2a.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-CIP2a.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-cip2b.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-cip2b.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-cip2b.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-CNR.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-CNR.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-CNR.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-CZFP1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-CZFP1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-CZFP1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-Dof4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-Dof4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-Dof4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-DREB3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-DREB3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-DREB3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-EIL1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-EIL1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-EIL1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-EIL2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-EIL2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-EIL2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-EIL3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-EIL3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-EIL3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-EIL4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-EIL4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-EIL4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-ERF10.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-ERF10.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-ERF10.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-ERF9.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-ERF9.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-ERF9.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-GRAS10.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-GRAS10.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-GRAS10.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-GRAS12.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-GRAS12.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-GRAS12.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-GRAS4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-GRAS4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-GRAS4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-gras6.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-gras6.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-gras6.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-JERF1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-JERF1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-JERF1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-LAT61.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-LAT61.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-LAT61.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-LES1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-LES1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-LES1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-LeT12.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-LeT12.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-LeT12.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-LeZIP2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-LeZIP2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-LeZIP2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-LOB1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-LOB1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-LOB1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-LOB38.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-LOB38.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-LOB38.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-LOB42.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-LOB42.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-LOB42.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-LSD1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-LSD1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-LSD1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-MADS1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-MADS1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-MADS1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-MADS-MC.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-MADS-MC.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-MADS-MC.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-MADS-RIN.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-MADS-RIN.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-MADS-RIN.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-MBD5.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-MBD5.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-MBD5.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-MBP7.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-MBP7.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-MBP7.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-NAC6.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-NAC6.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-NAC6.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-NAC-NOR.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-NAC-NOR.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-NAC-NOR.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-NF-YB-3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-NF-YB-3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-NF-YB-3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-PTI4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-PTI4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-PTI4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SCL32-like.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SCL32-like.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SCL32-like.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SEPALLATA3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SEPALLATA3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SEPALLATA3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlBEL1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlBEL1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlBEL1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlbHLH014.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlbHLH014.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlbHLH014.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlbHLH138.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlbHLH138.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlbHLH138.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlbHLH147.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlbHLH147.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlbHLH147.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlC3H11.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlC3H11.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlC3H11.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlC3H48.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlC3H48.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlC3H48.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlCOL1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlCOL1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlCOL1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlDof14.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlDof14.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlDof14.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlDRP1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlDRP1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlDRP1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlERF1a-1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlERF1a-1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlERF1a-1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlERF1a-2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlERF1a-2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlERF1a-2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlERF1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlERF1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlERF1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlERF36.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlERF36.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlERF36.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlERF4-1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlERF4-1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlERF4-1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlERF4-2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlERF4-2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlERF4-2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlERF5.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlERF5.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlERF5.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-Sl-ERF_C_4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-Sl-ERF_C_4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-Sl-ERF_C_4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-Sl-ERF_C_6.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-Sl-ERF_C_6.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-Sl-ERF_C_6.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-Sl-ERF_E_4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-Sl-ERF_E_4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-Sl-ERF_E_4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-Sl-ERF_F_2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-Sl-ERF_F_2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-Sl-ERF_F_2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-Sl-ERF_F_3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-Sl-ERF_F_3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-Sl-ERF_F_3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-Sl-ERF_F_4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-Sl-ERF_F_4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-Sl-ERF_F_4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-Sl-ERF_F_5.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-Sl-ERF_F_5.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-Sl-ERF_F_5.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlGABL2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlGABL2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlGABL2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlGABL4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlGABL4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlGABL4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlGATA9_1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlGATA9_1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlGATA9_1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlGATA9_2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlGATA9_2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlGATA9_2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlGRAS3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlGRAS3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlGRAS3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlGT2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlGT2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlGT2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlHB1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlHB1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlHB1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlHZIP2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlHZIP2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlHZIP2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlHZIP3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlHZIP3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlHZIP3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlMADF1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlMADF1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlMADF1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlMYB44.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlMYB44.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlMYB44.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlMYB70.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlMYB70.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlMYB70.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlMYB91.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlMYB91.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlMYB91.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlMYBL1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlMYBL1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlMYBL1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlMYBL2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlMYBL2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlMYBL2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlMYBL3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlMYBL3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlMYBL3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlMYBL4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlMYBL4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlMYBL4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlNAM1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlNAM1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlNAM1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlNAM2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlNAM2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlNAM2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlNAM3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlNAM3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlNAM3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlNAM4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlNAM4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlNAM4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlNAM5.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlNAM5.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlNAM5.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlTCP12.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlTCP12.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlTCP12.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlTCP15.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlTCP15.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlTCP15.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlTCP18.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlTCP18.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlTCP18.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlWOX14.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlWOX14.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlWOX14.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlWRKY11.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlWRKY11.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlWRKY11.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlWRKY23.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlWRKY23.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlWRKY23.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlWRKY40.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlWRKY40.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlWRKY40.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlWRKY41.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlWRKY41.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlWRKY41.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlWRKY6.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlWRKY6.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlWRKY6.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlWRKY7.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlWRKY7.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlWRKY7.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlWRKY81.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlWRKY81.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlWRKY81.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlYABBY2a.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlYABBY2a.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlYABBY2a.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlZF1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlZF1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlZF1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlZF2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlZF2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlZF2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlZF3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlZF3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlZF3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlZF6.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlZF6.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlZF6.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlZFCL3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlZFCL3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlZFCL3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlZIP1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlZIP1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlZIP1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlZIP3.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlZIP3.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlZIP3.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlZIP5.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlZIP5.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlZIP5.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlZIP6.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlZIP6.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlZIP6.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SlZIP7.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SlZIP7.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SlZIP7.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SolycHsfA2.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SolycHsfA2.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SolycHsfA2.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SolycHsfA4a.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SolycHsfA4a.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SolycHsfA4a.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SolycHsfA6b.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SolycHsfA6b.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SolycHsfA6b.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SolycHsfA7.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SolycHsfA7.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SolycHsfA7.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SolycHsfB1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SolycHsfB1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SolycHsfB1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SolycHsfB2a.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SolycHsfB2a.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SolycHsfB2a.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SolycHsfB2b.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SolycHsfB2b.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SolycHsfB2b.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-SolycHsfC1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-SolycHsfC1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-SolycHsfC1.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-TDR4.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-TDR4.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-TDR4.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-TM29.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-TM29.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-TM29.PE.a.MACS-2.1.0_peaks.RPM -RPM
python ~/code/bedRPKMfromBAM.py Red-VAHOX1.PE.a.MACS-2.1.0_peaks.narrowPeak.gz 0 Red-VAHOX1.PE.a.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Solanum_lycopersicum/Solanum_lycopersicum.SL2.40.19.chrom.sizes Red-VAHOX1.PE.a.MACS-2.1.0_peaks.RPM -RPM