cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/H3K27me3-Input-SRX323556.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes H3K27me3-Input-SRX323556.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/FIE-HA-Input-SRX323555.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes FIE-HA-Input-SRX323555.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/H3K27me3-SRX319031.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes H3K27me3-SRX319031.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/FIE-HA-SRX319030.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes FIE-HA-SRX319030.36mers.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/H3K27me3-Input-SRX323556.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes H3K27me3-Input-SRX323556.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/FIE-HA-Input-SRX323555.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes FIE-HA-Input-SRX323555.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/H3K27me3-SRX319031.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes H3K27me3-SRX319031.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/FIE-HA-SRX319030.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes FIE-HA-SRX319030.36mers.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/H3K27me3-Input-SRX323556.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes H3K27me3-Input-SRX323556.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/FIE-HA-Input-SRX323555.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes FIE-HA-Input-SRX323555.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/H3K27me3-SRX319031.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes H3K27me3-SRX319031.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/FIE-HA-SRX319030.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes FIE-HA-SRX319030.36mers.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/H3K27me3-Input-SRX323556.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes H3K27me3-Input-SRX323556.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/FIE-HA-Input-SRX323555.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes FIE-HA-Input-SRX323555.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/H3K27me3-SRX319031.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes H3K27me3-SRX319031.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/FIE-HA-SRX319030.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes FIE-HA-SRX319030.36mers.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/H3K27me3-Input-SRX323556.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes H3K27me3-Input-SRX323556.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/FIE-HA-Input-SRX323555.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes FIE-HA-Input-SRX323555.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/H3K27me3-SRX319031.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes H3K27me3-SRX319031.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/FIE-HA-SRX319030.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes FIE-HA-SRX319030.36mers.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/H3K27me3-Input-SRX323556.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes H3K27me3-Input-SRX323556.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/FIE-HA-Input-SRX323555.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes FIE-HA-Input-SRX323555.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/H3K27me3-SRX319031.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes H3K27me3-SRX319031.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
cd /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/; python /N/dc2/projects/marinovg/code/makewigglefromBAM-NH.py === /N/dc2/projects/marinovg/2013-10-22-Arabidopsis/51-organelles-only/FIE-HA-SRX319030.36mers.k3m2.bam /N/dc2/projects/marinovg/genomes/TAIR10/TAIR10.chrom.sizes FIE-HA-SRX319030.36mers.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast