python ~/code/SAMstats.py NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-NP_HSFA1b_NS_rep1-GSM2280210.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.unique.bam SAMstats-NP_HSFA1b_NS_rep1-GSM2280210 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-NP_HSFA1b_NS_rep2-GSM2280211.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.unique.bam SAMstats-NP_HSFA1b_NS_rep2-GSM2280211 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-NP_HSFA1b_HS_rep1-GSM2280212.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.unique.bam SAMstats-NP_HSFA1b_HS_rep1-GSM2280212 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-NP_HSFA1b_HS_rep2-GSM2280213.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.unique.bam SAMstats-NP_HSFA1b_HS_rep2-GSM2280213 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_control_NS_rep1-GSM2280214/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-NP_control_NS_rep1-GSM2280214.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.unique.bam SAMstats-NP_control_NS_rep1-GSM2280214 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_control_NS_rep2-GSM2280215/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-NP_control_NS_rep2-GSM2280215.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.unique.bam SAMstats-NP_control_NS_rep2-GSM2280215 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.unique.bam SAMstats-NP_control_HS_rep1-GSM2280216 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_control_HS_rep1-GSM2280216/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-NP_control_HS_rep1-GSM2280216.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_control_HS_rep2-GSM2280217/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-NP_control_HS_rep2-GSM2280217.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.unique.bam SAMstats-NP_control_HS_rep2-GSM2280217 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-35S_HSFA1b_NS_rep1-GSM2280218.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.unique.bam SAMstats-35S_HSFA1b_NS_rep1-GSM2280218 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-35S_HSFA1b_NS_rep2-GSM2280219.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.unique.bam SAMstats-35S_HSFA1b_NS_rep2-GSM2280219 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-35S_HSFA1b_HS_rep1-GSM2280220.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.unique.bam SAMstats-35S_HSFA1b_HS_rep1-GSM2280220 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-35S_HSFA1b_HS_rep2-GSM2280221.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.unique.bam SAMstats-35S_HSFA1b_HS_rep2-GSM2280221 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_control_NS_rep1-GSM2280222/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-35S_control_NS_rep1-GSM2280222.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.unique.bam SAMstats-35S_control_NS_rep1-GSM2280222 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_control_NS_rep2-GSM2280223/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-35S_control_NS_rep2-GSM2280223.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.unique.bam SAMstats-35S_control_NS_rep2-GSM2280223 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_control_HS_rep1-GSM2280224/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-35S_control_HS_rep1-GSM2280224.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.unique.bam SAMstats-35S_control_HS_rep1-GSM2280224 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_control_HS_rep2-GSM2280225/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-35S_control_HS_rep2-GSM2280225.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py 35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.unique.bam SAMstats-35S_control_HS_rep2-GSM2280225 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
Rscript ~/code/spp/spp_package/run_spp.R -c=NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.QC &
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep1-GSM2280210/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_NS_rep2-GSM2280211/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep1-GSM2280212/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_HSFA1b_HS_rep2-GSM2280213/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep1-GSM2280214/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep1-GSM2280214/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep1-GSM2280214/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep1-GSM2280214/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep1-GSM2280214/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep1-GSM2280214/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep1-GSM2280214/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep1-GSM2280214/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep1-GSM2280214/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep1-GSM2280214/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep1-GSM2280214/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep1-GSM2280214/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep1-GSM2280214/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep2-GSM2280215/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep2-GSM2280215/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep2-GSM2280215/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep2-GSM2280215/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep2-GSM2280215/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep2-GSM2280215/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep2-GSM2280215/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep2-GSM2280215/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep2-GSM2280215/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep2-GSM2280215/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep2-GSM2280215/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep2-GSM2280215/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_NS_rep2-GSM2280215/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep1-GSM2280216/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep1-GSM2280216/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep1-GSM2280216/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep1-GSM2280216/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep1-GSM2280216/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep1-GSM2280216/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep1-GSM2280216/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep1-GSM2280216/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep1-GSM2280216/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep1-GSM2280216/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep1-GSM2280216/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep1-GSM2280216/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep1-GSM2280216/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep2-GSM2280217/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep2-GSM2280217/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep2-GSM2280217/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep2-GSM2280217/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep2-GSM2280217/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep2-GSM2280217/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep2-GSM2280217/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep2-GSM2280217/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep2-GSM2280217/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep2-GSM2280217/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep2-GSM2280217/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep2-GSM2280217/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes NP_control_HS_rep2-GSM2280217/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep1-GSM2280218/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_NS_rep2-GSM2280219/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep1-GSM2280220/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_HSFA1b_HS_rep2-GSM2280221/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep1-GSM2280222/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep1-GSM2280222/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep1-GSM2280222/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep1-GSM2280222/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep1-GSM2280222/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep1-GSM2280222/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep1-GSM2280222/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep1-GSM2280222/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep1-GSM2280222/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep1-GSM2280222/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep1-GSM2280222/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep1-GSM2280222/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep1-GSM2280222/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep2-GSM2280223/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep2-GSM2280223/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep2-GSM2280223/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep2-GSM2280223/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep2-GSM2280223/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep2-GSM2280223/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep2-GSM2280223/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep2-GSM2280223/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep2-GSM2280223/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep2-GSM2280223/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep2-GSM2280223/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep2-GSM2280223/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_NS_rep2-GSM2280223/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep1-GSM2280224/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep1-GSM2280224/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep1-GSM2280224/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep1-GSM2280224/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep1-GSM2280224/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep1-GSM2280224/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep1-GSM2280224/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep1-GSM2280224/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep1-GSM2280224/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep1-GSM2280224/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep1-GSM2280224/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep1-GSM2280224/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep1-GSM2280224/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep2-GSM2280225/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep2-GSM2280225/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep2-GSM2280225/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep2-GSM2280225/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep2-GSM2280225/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep2-GSM2280225/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep2-GSM2280225/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep2-GSM2280225/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep2-GSM2280225/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep2-GSM2280225/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep2-GSM2280225/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep2-GSM2280225/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === 35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes 35S_control_HS_rep2-GSM2280225/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM