cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_GFP-Trap-GSM1701078.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_anti-TRB1-GSM1701080.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_GFP-Trap-GSM1701078.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_anti-TRB1-GSM1701080.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_GFP-Trap-GSM1701078.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_anti-TRB1-GSM1701080.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_GFP-Trap-GSM1701078.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_anti-TRB1-GSM1701080.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_GFP-Trap-GSM1701078.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_anti-TRB1-GSM1701080.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_GFP-Trap-GSM1701078.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078.36mers.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.36mers.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_Wt-_anti-TRB1-GSM1701080.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080.36mers.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/66-organelles-nucleus-merged-k3m2/TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081.36mers.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast