cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_Input-GSM1035301.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes 29CHIP_Input-GSM1035301.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_mock-GSM1035302.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes 29CHIP_mock-GSM1035302.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/MADS29-CHIP_IPsample-GSM1035300.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes MADS29-CHIP_IPsample-GSM1035300.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_Input-GSM1035301.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes 29CHIP_Input-GSM1035301.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_mock-GSM1035302.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes 29CHIP_mock-GSM1035302.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/MADS29-CHIP_IPsample-GSM1035300.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes MADS29-CHIP_IPsample-GSM1035300.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_Input-GSM1035301.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes 29CHIP_Input-GSM1035301.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_mock-GSM1035302.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes 29CHIP_mock-GSM1035302.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/MADS29-CHIP_IPsample-GSM1035300.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes MADS29-CHIP_IPsample-GSM1035300.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_Input-GSM1035301.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes 29CHIP_Input-GSM1035301.36mers.chrP.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_mock-GSM1035302.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes 29CHIP_mock-GSM1035302.36mers.chrP.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/MADS29-CHIP_IPsample-GSM1035300.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes MADS29-CHIP_IPsample-GSM1035300.36mers.chrP.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_Input-GSM1035301.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes 29CHIP_Input-GSM1035301.36mers.chrP.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_mock-GSM1035302.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes 29CHIP_mock-GSM1035302.36mers.chrP.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/MADS29-CHIP_IPsample-GSM1035300.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes MADS29-CHIP_IPsample-GSM1035300.36mers.chrP.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_Input-GSM1035301.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes 29CHIP_Input-GSM1035301.36mers.chrP.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/29CHIP_mock-GSM1035302.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes 29CHIP_mock-GSM1035302.36mers.chrP.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrP
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/54-Oryza_sativa-organelles-nucleus-merged-k3m2/MADS29-CHIP_IPsample-GSM1035300.36mers.bam /N/dc2/projects/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes MADS29-CHIP_IPsample-GSM1035300.36mers.chrP.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrP