cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_input-GSM1517647.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep1_input-GSM1517647.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_FEA4_ChIP-GSM1517648.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep1_FEA4_ChIP-GSM1517648.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_input-GSM1517649.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep2_input-GSM1517649.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_FEA4_ChIP-GSM1517650.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep2_FEA4_ChIP-GSM1517650.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_input-GSM1517647.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep1_input-GSM1517647.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_FEA4_ChIP-GSM1517648.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep1_FEA4_ChIP-GSM1517648.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_input-GSM1517649.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep2_input-GSM1517649.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_FEA4_ChIP-GSM1517650.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep2_FEA4_ChIP-GSM1517650.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_input-GSM1517647.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep1_input-GSM1517647.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_FEA4_ChIP-GSM1517648.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep1_FEA4_ChIP-GSM1517648.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_input-GSM1517649.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep2_input-GSM1517649.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_FEA4_ChIP-GSM1517650.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep2_FEA4_ChIP-GSM1517650.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_input-GSM1517647.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep1_input-GSM1517647.36mers.chrP.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_FEA4_ChIP-GSM1517648.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep1_FEA4_ChIP-GSM1517648.36mers.chrP.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_input-GSM1517649.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep2_input-GSM1517649.36mers.chrP.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_FEA4_ChIP-GSM1517650.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep2_FEA4_ChIP-GSM1517650.36mers.chrP.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_input-GSM1517647.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep1_input-GSM1517647.36mers.chrP.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_FEA4_ChIP-GSM1517648.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep1_FEA4_ChIP-GSM1517648.36mers.chrP.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_input-GSM1517649.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep2_input-GSM1517649.36mers.chrP.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_FEA4_ChIP-GSM1517650.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep2_FEA4_ChIP-GSM1517650.36mers.chrP.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_input-GSM1517647.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep1_input-GSM1517647.36mers.chrP.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep1_FEA4_ChIP-GSM1517648.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep1_FEA4_ChIP-GSM1517648.36mers.chrP.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_input-GSM1517649.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep2_input-GSM1517649.36mers.chrP.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/52-Zea_mays-organelles-nucleus-merged-k3m2/rep2_FEA4_ChIP-GSM1517650.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Zea_mays.AGPv3/Zea_mays.AGPv3.chrom.sizes rep2_FEA4_ChIP-GSM1517650.36mers.chrP.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrP