python ~/code/SAMstats.py GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-GFP_Dex_6h_ChIP-GSM2131011.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.unique.bam SAMstats-GFP_Dex_6h_ChIP-GSM2131011 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.unique.bam SAMstats-AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.chrM+chloroplast.k3m2.bam SAMstats-AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013.chrM+chloroplast.k3m2 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
python ~/code/SAMstats.py AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.unique.bam SAMstats-AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013 -bam ~/genomes/TAIR10/TAIR10.chrom.sizes samtools
Rscript ~/code/spp/spp_package/run_spp.R -c=GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.QC &
Rscript ~/code/spp/spp_package/run_spp.R -c=AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.unique.bam -p=8 -savp -rf -s=-0:2:400 -out=AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.QC &
python ~/code/makewigglefromBAM-NH.py === GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes GFP_Dex_6h_ChIP-GSM2131011/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT3G45810_DIG1_Dex_6h_ChIP-GSM2131012/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.chrM+chloroplast.k3m2.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast
python ~/code/makewigglefromBAM-NH.py === AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.chrM+chloroplast.k3m2.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.chrM+chloroplast.k3m2.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.chrM+chloroplast.k3m2.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.chrM+chloroplast.k3m2.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM
python ~/code/makewigglefromBAM-NH.py === AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.unique.chloroplast.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.unique.chloroplast.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.unique.chloroplast.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chloroplast -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.unique.chrM.minus.RPM.wig -RPM -stranded - -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.unique.chrM.plus.RPM.wig -RPM -stranded + -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM
python ~/code/makewigglefromBAM-NH.py === AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.unique.bam ~/genomes/TAIR10/TAIR10.chrom.sizes AT5G50360_DIG2_Dex_6h_ChIP-GSM2131013/all.1x36mers.TAIR10.unique.chrM.RPM.wig -RPM -notitle -singlebasepair -mismatchesMD 0 -chr chrM -uniqueBAM