cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_1-GSM1463808.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_BLJ_YFP_1-GSM1463808.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_2-GSM1463810.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_BLJ_YFP_2-GSM1463810.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_1-GSM1463812.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_JKD_YFP_1-GSM1463812.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_2-GSM1463814.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_JKD_YFP_2-GSM1463814.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_Control-GSM1463816.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_Control-GSM1463816.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_1-GSM1463808.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_BLJ_YFP_1-GSM1463808.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_2-GSM1463810.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_BLJ_YFP_2-GSM1463810.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_1-GSM1463812.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_JKD_YFP_1-GSM1463812.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_2-GSM1463814.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_JKD_YFP_2-GSM1463814.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_Control-GSM1463816.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_Control-GSM1463816.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_1-GSM1463808.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_BLJ_YFP_1-GSM1463808.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_2-GSM1463810.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_BLJ_YFP_2-GSM1463810.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_1-GSM1463812.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_JKD_YFP_1-GSM1463812.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_2-GSM1463814.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_JKD_YFP_2-GSM1463814.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_Control-GSM1463816.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_Control-GSM1463816.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_1-GSM1463808.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_BLJ_YFP_1-GSM1463808.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_2-GSM1463810.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_BLJ_YFP_2-GSM1463810.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_1-GSM1463812.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_JKD_YFP_1-GSM1463812.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_2-GSM1463814.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_JKD_YFP_2-GSM1463814.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_Control-GSM1463816.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_Control-GSM1463816.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_1-GSM1463808.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_BLJ_YFP_1-GSM1463808.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_2-GSM1463810.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_BLJ_YFP_2-GSM1463810.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_1-GSM1463812.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_JKD_YFP_1-GSM1463812.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_2-GSM1463814.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_JKD_YFP_2-GSM1463814.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_Control-GSM1463816.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_Control-GSM1463816.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_1-GSM1463808.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_BLJ_YFP_1-GSM1463808.36mers.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_BLJ_YFP_2-GSM1463810.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_BLJ_YFP_2-GSM1463810.36mers.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_1-GSM1463812.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_JKD_YFP_1-GSM1463812.36mers.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_JKD_YFP_2-GSM1463814.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_JKD_YFP_2-GSM1463814.36mers.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/62-organelles-nucleus-merged-k3m2/At_Control-GSM1463816.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes At_Control-GSM1463816.36mers.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast