python ~/code/SAMstats.py JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.unique.bam SAMstats-JAG-GFP-replicate-1-GSM1247499 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py JAG-GFP-replicate-1-GSM1247499/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-JAG-GFP-replicate-1-GSM1247499.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.unique.bam SAMstats-JAG-GFP-replicate-2-GSM1247500 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py JAG-GFP-replicate-2-GSM1247500/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-JAG-GFP-replicate-2-GSM1247500.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.unique.bam SAMstats-JAG-GFP-replicate-3-GSM1247501 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py JAG-GFP-replicate-3-GSM1247501/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-JAG-GFP-replicate-3-GSM1247501.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.unique.bam SAMstats-JAG-wild-type-replicate-1-GSM1247502 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-JAG-wild-type-replicate-1-GSM1247502.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.unique.bam SAMstats-JAG-wild-type-replicate-2-GSM1247503 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-JAG-wild-type-replicate-2-GSM1247503.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.unique.bam SAMstats-JAG-wild-type-replicate-3-GSM1247504 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-JAG-wild-type-replicate-3-GSM1247504.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
Rscript ~/code/spp/spp_package/run_spp.R -c=JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.QC &
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-1-GSM1247499/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-1-GSM1247499/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-1-GSM1247499/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-1-GSM1247499/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-1-GSM1247499/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-1-GSM1247499/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-1-GSM1247499/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-1-GSM1247499/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-1-GSM1247499/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-1-GSM1247499/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-1-GSM1247499/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-1-GSM1247499/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-1-GSM1247499/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-2-GSM1247500/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-2-GSM1247500/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-2-GSM1247500/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-2-GSM1247500/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-2-GSM1247500/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-2-GSM1247500/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-2-GSM1247500/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-2-GSM1247500/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-2-GSM1247500/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-2-GSM1247500/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-2-GSM1247500/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-2-GSM1247500/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-2-GSM1247500/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-3-GSM1247501/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-3-GSM1247501/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-3-GSM1247501/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-3-GSM1247501/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-3-GSM1247501/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-3-GSM1247501/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-3-GSM1247501/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-3-GSM1247501/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-3-GSM1247501/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-3-GSM1247501/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-3-GSM1247501/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-GFP-replicate-3-GSM1247501/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-GFP-replicate-3-GSM1247501/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-1-GSM1247502/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-2-GSM1247503/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes JAG-wild-type-replicate-3-GSM1247504/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM