cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1-GSM1348068.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE3-1-GSM1348068.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1_input-GSM1348069.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE3-1_input-GSM1348069.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1-GSM1348070.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE9-1-GSM1348070.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1_inout-GSM1348071.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE9-1_inout-GSM1348071.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4-GSM1348072.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE17-4-GSM1348072.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4_input-GSM1348073.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE17-4_input-GSM1348073.36mers.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1-GSM1348068.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE3-1-GSM1348068.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1_input-GSM1348069.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE3-1_input-GSM1348069.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1-GSM1348070.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE9-1-GSM1348070.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1_inout-GSM1348071.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE9-1_inout-GSM1348071.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4-GSM1348072.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE17-4-GSM1348072.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4_input-GSM1348073.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE17-4_input-GSM1348073.36mers.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1-GSM1348068.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE3-1-GSM1348068.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1_input-GSM1348069.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE3-1_input-GSM1348069.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1-GSM1348070.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE9-1-GSM1348070.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1_inout-GSM1348071.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE9-1_inout-GSM1348071.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4-GSM1348072.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE17-4-GSM1348072.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4_input-GSM1348073.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE17-4_input-GSM1348073.36mers.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1-GSM1348068.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE3-1-GSM1348068.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1_input-GSM1348069.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE3-1_input-GSM1348069.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1-GSM1348070.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE9-1-GSM1348070.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1_inout-GSM1348071.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE9-1_inout-GSM1348071.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4-GSM1348072.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE17-4-GSM1348072.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4_input-GSM1348073.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE17-4_input-GSM1348073.36mers.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1-GSM1348068.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE3-1-GSM1348068.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1_input-GSM1348069.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE3-1_input-GSM1348069.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1-GSM1348070.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE9-1-GSM1348070.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1_inout-GSM1348071.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE9-1_inout-GSM1348071.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4-GSM1348072.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE17-4-GSM1348072.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4_input-GSM1348073.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE17-4_input-GSM1348073.36mers.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE3-1_input-GSM1348069.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE3-1_input-GSM1348069.36mers.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1-GSM1348070.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE9-1-GSM1348070.36mers.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE9-1_inout-GSM1348071.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE9-1_inout-GSM1348071.36mers.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4-GSM1348072.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE17-4-GSM1348072.36mers.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/58-organelles-nucleus-merged-k3m2/AtDEK3_OE17-4_input-GSM1348073.36mers.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes AtDEK3_OE17-4_input-GSM1348073.36mers.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast