python ~/code/SAMstats.py PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.bam SAMstats-PolIV-ChIP-GSM1103231 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.unique.bam SAMstats-PolIV-ChIP-replicate-2-GSM1103233 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.unique.bam SAMstats-shh1-PolIV-ChIP-replicate-2-GSM1103234 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.unique.bam SAMstats-Columbia-ChIP-GSM1103230 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.unique.bam SAMstats-Columbia-ChIP-replicate-2-GSM1103232 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py PolIV-ChIP-GSM1103231/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-PolIV-ChIP-GSM1103231.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-PolIV-ChIP-replicate-2-GSM1103233.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-shh1-PolIV-ChIP-replicate-2-GSM1103234.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Columbia-ChIP-GSM1103230/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-Columbia-ChIP-GSM1103230.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-Columbia-ChIP-replicate-2-GSM1103232.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
Rscript ~/code/spp/spp_package/run_spp.R -c=PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.QC &
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-GSM1103230/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-GSM1103231/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-GSM1103231/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-GSM1103230/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-GSM1103230/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-GSM1103231/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-GSM1103231/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-GSM1103230/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-GSM1103230/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-GSM1103231/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-GSM1103231/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-GSM1103230/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-GSM1103230/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-GSM1103231/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-GSM1103231/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-GSM1103230/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-GSM1103230/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-GSM1103231/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-GSM1103231/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-GSM1103230/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-GSM1103230/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-GSM1103231/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-GSM1103231/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes PolIV-ChIP-replicate-2-GSM1103233/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes shh1-PolIV-ChIP-replicate-2-GSM1103234/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-GSM1103230/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-GSM1103230/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes Columbia-ChIP-replicate-2-GSM1103232/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast