cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-1-GSM1059957.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-1-GSM1059957.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-2-GSM1059958.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-2-GSM1059958.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-3-GSM1059959.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-3-GSM1059959.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-1-GSM1059960.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-1-GSM1059960.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-2-GSM1059961.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-2-GSM1059961.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-3-GSM1059962.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-3-GSM1059962.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-1-GSM1059963.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-1-GSM1059963.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-2-GSM1059964.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-2-GSM1059964.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-3-GSM1059965.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-3-GSM1059965.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-1A-GSM1059966.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-1A-GSM1059966.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-2A-GSM1059967.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-2A-GSM1059967.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-3A-GSM1059968.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-3A-GSM1059968.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-1-GSM1059957.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-1-GSM1059957.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-2-GSM1059958.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-2-GSM1059958.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-3-GSM1059959.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-3-GSM1059959.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-1-GSM1059960.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-1-GSM1059960.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-2-GSM1059961.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-2-GSM1059961.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-3-GSM1059962.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-3-GSM1059962.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-1-GSM1059963.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-1-GSM1059963.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-2-GSM1059964.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-2-GSM1059964.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-3-GSM1059965.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-3-GSM1059965.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-1A-GSM1059966.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-1A-GSM1059966.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-2A-GSM1059967.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-2A-GSM1059967.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-3A-GSM1059968.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-3A-GSM1059968.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-1-GSM1059957.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-1-GSM1059957.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-2-GSM1059958.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-2-GSM1059958.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-3-GSM1059959.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-3-GSM1059959.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-1-GSM1059960.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-1-GSM1059960.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-2-GSM1059961.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-2-GSM1059961.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-3-GSM1059962.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-3-GSM1059962.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-1-GSM1059963.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-1-GSM1059963.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-2-GSM1059964.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-2-GSM1059964.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-3-GSM1059965.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-3-GSM1059965.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-1A-GSM1059966.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-1A-GSM1059966.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-2A-GSM1059967.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-2A-GSM1059967.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-3A-GSM1059968.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-3A-GSM1059968.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-1-GSM1059957.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-1-GSM1059957.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-2-GSM1059958.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-2-GSM1059958.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-3-GSM1059959.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-3-GSM1059959.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-1-GSM1059960.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-1-GSM1059960.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-2-GSM1059961.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-2-GSM1059961.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-3-GSM1059962.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-3-GSM1059962.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-1-GSM1059963.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-1-GSM1059963.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-2-GSM1059964.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-2-GSM1059964.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-3-GSM1059965.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-3-GSM1059965.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-1A-GSM1059966.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-1A-GSM1059966.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-2A-GSM1059967.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-2A-GSM1059967.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-3A-GSM1059968.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-3A-GSM1059968.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-1-GSM1059957.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-1-GSM1059957.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-2-GSM1059958.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-2-GSM1059958.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-3-GSM1059959.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-3-GSM1059959.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-1-GSM1059960.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-1-GSM1059960.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-2-GSM1059961.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-2-GSM1059961.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-3-GSM1059962.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-3-GSM1059962.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-1-GSM1059963.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-1-GSM1059963.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-2-GSM1059964.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-2-GSM1059964.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-3-GSM1059965.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-3-GSM1059965.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-1A-GSM1059966.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-1A-GSM1059966.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-2A-GSM1059967.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-2A-GSM1059967.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-3A-GSM1059968.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-3A-GSM1059968.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-1-GSM1059957.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-1-GSM1059957.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-2-GSM1059958.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-2-GSM1059958.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF1-peaks-3-GSM1059959.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF1-peaks-3-GSM1059959.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-1-GSM1059960.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-1-GSM1059960.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-2-GSM1059961.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-2-GSM1059961.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-3-GSM1059962.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-3-GSM1059962.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-1-GSM1059963.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-1-GSM1059963.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-2-GSM1059964.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-2-GSM1059964.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/PIF4-peaks-3-GSM1059965.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes PIF4-peaks-3-GSM1059965.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-1A-GSM1059966.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-1A-GSM1059966.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-2A-GSM1059967.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-2A-GSM1059967.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/48-organelles-only/WT-ChIP-3A-GSM1059968.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes WT-ChIP-3A-GSM1059968.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast