python ~/code/SAMstats.py RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.unique.bam SAMstats-RGA_ChIP1-GSM1429897 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py RGA_ChIP1-GSM1429897/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-RGA_ChIP1-GSM1429897.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.unique.bam SAMstats-RGA_ChIP2-GSM1429898 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py RGA_ChIP2-GSM1429898/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-RGA_ChIP2-GSM1429898.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.unique.bam SAMstats-RGA_ChIP3-GSM1429899 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py RGA_ChIP3-GSM1429899/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-RGA_ChIP3-GSM1429899.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.unique.bam SAMstats-WT_ChIP1-GSM1429900 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py WT_ChIP1-GSM1429900/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-WT_ChIP1-GSM1429900.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.unique.bam SAMstats-WT_ChIP2-GSM1429901 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py WT_ChIP2-GSM1429901/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-WT_ChIP2-GSM1429901.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.unique.bam SAMstats-WT_ChIP3-GSM1429902 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py WT_ChIP3-GSM1429902/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-WT_ChIP3-GSM1429902.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
Rscript ~/code/spp/spp_package/run_spp.R -c=RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.QC &
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP1-GSM1429897/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP1-GSM1429897/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP1-GSM1429897/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP1-GSM1429897/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP1-GSM1429897/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP1-GSM1429897/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP1-GSM1429897/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP1-GSM1429897/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP1-GSM1429897/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP1-GSM1429897/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP1-GSM1429897/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP1-GSM1429897/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP1-GSM1429897/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP2-GSM1429898/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP2-GSM1429898/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP2-GSM1429898/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP2-GSM1429898/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP2-GSM1429898/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP2-GSM1429898/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP2-GSM1429898/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP2-GSM1429898/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP2-GSM1429898/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP2-GSM1429898/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP2-GSM1429898/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP2-GSM1429898/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP2-GSM1429898/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP3-GSM1429899/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP3-GSM1429899/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP3-GSM1429899/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP3-GSM1429899/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP3-GSM1429899/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP3-GSM1429899/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP3-GSM1429899/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP3-GSM1429899/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP3-GSM1429899/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP3-GSM1429899/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === RGA_ChIP3-GSM1429899/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes RGA_ChIP3-GSM1429899/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP1-GSM1429900/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP1-GSM1429900/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP1-GSM1429900/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === WT_ChIP1-GSM1429900/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP1-GSM1429900/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === WT_ChIP1-GSM1429900/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP1-GSM1429900/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === WT_ChIP1-GSM1429900/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP1-GSM1429900/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP1-GSM1429900/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP1-GSM1429900/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP1-GSM1429900/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP1-GSM1429900/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP2-GSM1429901/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP2-GSM1429901/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP2-GSM1429901/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === WT_ChIP2-GSM1429901/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP2-GSM1429901/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === WT_ChIP2-GSM1429901/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP2-GSM1429901/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === WT_ChIP2-GSM1429901/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP2-GSM1429901/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP2-GSM1429901/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP2-GSM1429901/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP2-GSM1429901/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP2-GSM1429901/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP3-GSM1429902/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP3-GSM1429902/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP3-GSM1429902/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === WT_ChIP3-GSM1429902/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP3-GSM1429902/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === WT_ChIP3-GSM1429902/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP3-GSM1429902/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === WT_ChIP3-GSM1429902/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP3-GSM1429902/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP3-GSM1429902/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP3-GSM1429902/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === WT_ChIP3-GSM1429902/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes WT_ChIP3-GSM1429902/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM