python ~/code/SAMstats.py prr7-3_Input_ExpI-GSM1196645/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-prr7-3_Input_ExpI-GSM1196645.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique.bam SAMstats-prr7-3_Input_ExpI-GSM1196645 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py prr7-3_IP_ExpI-GSM1196646/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-prr7-3_IP_ExpI-GSM1196646.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique.bam SAMstats-prr7-3_IP_ExpI-GSM1196646 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique.bam SAMstats-prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique.bam SAMstats-prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique.bam SAMstats-prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique.bam SAMstats-prr7-3_IP_ExpII-GSM1196650 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py prr7-3_IP_ExpII-GSM1196650/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-prr7-3_IP_ExpII-GSM1196650.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
Rscript ~/code/spp/spp_package/run_spp.R -c=prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.QC &
python ~/code/makewigglefromBAM-NH.py === prr7-3_Input_ExpI-GSM1196645/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_Input_ExpI-GSM1196645/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_Input_ExpI-GSM1196645/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_Input_ExpI-GSM1196645/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_Input_ExpI-GSM1196645/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_Input_ExpI-GSM1196645/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_Input_ExpI-GSM1196645/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_Input_ExpI-GSM1196645/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_Input_ExpI-GSM1196645/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_Input_ExpI-GSM1196645/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_Input_ExpI-GSM1196645/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_Input_ExpI-GSM1196645/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_Input_ExpI-GSM1196645/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpI-GSM1196646/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpI-GSM1196646/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpI-GSM1196646/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpI-GSM1196646/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpI-GSM1196646/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpI-GSM1196646/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpI-GSM1196646/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpI-GSM1196646/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpI-GSM1196646/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpI-GSM1196646/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpI-GSM1196646/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpI-GSM1196646/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpI-GSM1196646/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_Input_ExpI-GSM1196647/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpI-GSM1196648/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_PRR7_HA-PRR7_151_IP_ExpII-GSM1196649/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpII-GSM1196650/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpII-GSM1196650/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpII-GSM1196650/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpII-GSM1196650/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpII-GSM1196650/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpII-GSM1196650/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpII-GSM1196650/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpII-GSM1196650/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpII-GSM1196650/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpII-GSM1196650/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpII-GSM1196650/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpII-GSM1196650/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes prr7-3_IP_ExpII-GSM1196650/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM