python ~/code/SAMstats.py SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.unique.bam SAMstats-SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.unique.bam SAMstats-SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.unique.bam SAMstats-AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.unique.bam SAMstats-AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.unique.bam SAMstats-AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.unique.bam SAMstats-mock-ChIP-control-2d-GSM1142629 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py mock-ChIP-control-2d-GSM1142629/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-mock-ChIP-control-2d-GSM1142629.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.unique.bam SAMstats-mock-ChIP-control-4d-GSM1142630 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py mock-ChIP-control-4d-GSM1142630/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-mock-ChIP-control-4d-GSM1142630.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.unique.bam SAMstats-mock-ChIP-control-8d-GSM1142631 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py mock-ChIP-control-8d-GSM1142631/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-mock-ChIP-control-8d-GSM1142631.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.unique.bam SAMstats-AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.unique.bam SAMstats-SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.unique.bam SAMstats-SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
Rscript ~/code/spp/spp_package/run_spp.R -c=SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.QC &
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-2d-GSM1142629/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-2d-GSM1142629/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-2d-GSM1142629/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-2d-GSM1142629/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-2d-GSM1142629/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-2d-GSM1142629/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-2d-GSM1142629/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-2d-GSM1142629/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-2d-GSM1142629/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-2d-GSM1142629/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-2d-GSM1142629/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-2d-GSM1142629/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-2d-GSM1142629/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-4d-GSM1142630/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-4d-GSM1142630/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-4d-GSM1142630/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-4d-GSM1142630/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-4d-GSM1142630/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-4d-GSM1142630/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-4d-GSM1142630/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-4d-GSM1142630/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-4d-GSM1142630/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-4d-GSM1142630/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-4d-GSM1142630/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-4d-GSM1142630/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-4d-GSM1142630/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-8d-GSM1142631/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-8d-GSM1142631/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-8d-GSM1142631/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-8d-GSM1142631/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-8d-GSM1142631/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-8d-GSM1142631/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-8d-GSM1142631/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-8d-GSM1142631/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-8d-GSM1142631/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-8d-GSM1142631/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-8d-GSM1142631/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === mock-ChIP-control-8d-GSM1142631/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes mock-ChIP-control-8d-GSM1142631/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM