python ~/code/SAMstats.py Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.unique.bam SAMstats-Inflorescence_svp_SVP-GFP_rep1-GSM820411 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.unique.bam SAMstats-Inflorescence_svp_SVP-GFP_rep2-GSM820412 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.unique.bam SAMstats-seedling_svp_SVP-GFP_rep1-GSM820413 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.unique.bam SAMstats-seedling_svp_SVP-GFP_rep2-GSM820414 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.unique.bam SAMstats-Inflorescence_wt-col_rep1-GSM820415 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.unique.bam SAMstats-Inflorescence_wt-col_rep2-GSM820416 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-Inflorescence_svp_SVP-GFP_rep1-GSM820411.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-Inflorescence_svp_SVP-GFP_rep2-GSM820412.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-seedling_svp_SVP-GFP_rep1-GSM820413.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-seedling_svp_SVP-GFP_rep2-GSM820414.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-Inflorescence_wt-col_rep1-GSM820415.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-Inflorescence_wt-col_rep2-GSM820416.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
Rscript ~/code/spp/spp_package/run_spp.R -c=Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.QC &
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep1-GSM820411/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_svp_SVP-GFP_rep2-GSM820412/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep1-GSM820413/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes seedling_svp_SVP-GFP_rep2-GSM820414/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep1-GSM820415/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Inflorescence_wt-col_rep2-GSM820416/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast