python ~/code/SAMstats.py ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-ChIPSeq-ABI5_Ab-GSM1466341.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.unique.bam SAMstats-ChIPSeq-ABI5_Ab-GSM1466341 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-ChIPSeq-IgG_mock-GSM1466342.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.unique.bam SAMstats-ChIPSeq-IgG_mock-GSM1466342 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-ChIPSeq-ABI5_Ypet_1-GSM1466343.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.unique.bam SAMstats-ChIPSeq-ABI5_Ypet_1-GSM1466343 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-ChIPSeq-ABI5_mock_1-GSM1466344.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.unique.bam SAMstats-ChIPSeq-ABI5_mock_1-GSM1466344 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-ChIPSeq-ABI5_Ypet_2-GSM1466345.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.unique.bam SAMstats-ChIPSeq-ABI5_Ypet_2-GSM1466345 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-ChIPSeq-ABI5_mock_2-GSM1466346.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.unique.bam SAMstats-ChIPSeq-ABI5_mock_2-GSM1466346 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
Rscript ~/code/spp/spp_package/run_spp.R -c=ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.QC &
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ab-GSM1466341/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-IgG_mock-GSM1466342/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_1-GSM1466343/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_1-GSM1466344/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_Ypet_2-GSM1466345/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes ChIPSeq-ABI5_mock_2-GSM1466346/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM