python ~/code/SAMstats.py TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-TRB1_Wt-_GFP-Trap-GSM1701078.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.unique.bam SAMstats-TRB1_Wt-_GFP-Trap-GSM1701078 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-TRB1_TRB1-GFP+_GFP-Trap-GSM1701079.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.unique.bam SAMstats-TRB1_TRB1-GFP+_GFP-Trap-GSM1701079 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-TRB1_Wt-_anti-TRB1-GSM1701080.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.unique.bam SAMstats-TRB1_Wt-_anti-TRB1-GSM1701080 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-TRB1_TRB1+_anti-TRB1-GSM1701081.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.unique.bam SAMstats-TRB1_TRB1+_anti-TRB1-GSM1701081 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
Rscript ~/code/spp/spp_package/run_spp.R -c=TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.QC &
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_GFP-Trap-GSM1701078/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1-GFP+_GFP-Trap-GSM1701079/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_Wt-_anti-TRB1-GSM1701080/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes TRB1_TRB1+_anti-TRB1-GSM1701081/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM